Example Workflow
1. Load the Package
library(TaxoTools)
#> Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading
#> 'TaxoTools'
#> Warning: replacing previous import 'graphics::layout' by 'plotly::layout' when
#> loading 'TaxoTools'
#> Warning: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot'
#> when loading 'TaxoTools'
#> Warning: replacing previous import 'phytools::rescale' by 'scales::rescale'
#> when loading 'TaxoTools'
#> Warning: replacing previous import 'scales::viridis_pal' by
#> 'viridis::viridis_pal' when loading 'TaxoTools'
#> Warning: replacing previous import 'rlang::as_list' by 'xml2::as_list' when
#> loading 'TaxoTools'
#> Registered S3 method overwritten by 'GGally':
#> method from
#> +.gg ggplot2
library(ape)
#> Warning: package 'ape' was built under R version 4.3.3
library(phytools)
#> Warning: package 'phytools' was built under R version 4.3.3
#> Loading required package: maps
#> Warning: package 'maps' was built under R version 4.3.32. Load example data and root the trees
Load the Sauresia time tree
sauresia_Time <- read.tree("C:\\Users\\mschools\\Documents\\TaxoTools\\vignettes\\examples\\sauresia_48tx_timetree.nwk")
plot(sauresia_Time)
Load, root, and check the ML Sauresia tree
sauresia_ML <- read.tree("C:\\Users\\mschools\\Documents\\TaxoTools\\vignettes\\examples\\sauresia_48tx_IQtree_rooted.nwk")
sauresia_ML_rooted <- reroot(
sauresia_ML,
48,
position = sauresia_ML$edge.length[which(sauresia_ML$edge[,2]==48)]/2)
is.rooted(sauresia_ML_rooted)
#> [1] TRUE
plot(sauresia_ML_rooted, show.node.label = T)
Load, root, and check the Bayesian Sauresia tree
sauresia_B <- read.tree("C:\\Users\\mschools\\Documents\\TaxoTools\\vignettes\\examples\\sauresia_48tx_MrBayes_rooted.nwk")
sauresia_B_rooted <- reroot(
sauresia_B,
48,
position = sauresia_B$edge.length[which(sauresia_B$edge[,2]==48)]/2)
is.rooted(sauresia_B_rooted)
#> [1] TRUE
plot(sauresia_B_rooted, show.node.label = T)
Load in Sauresia morphodata and metadata (unclean and clean version)
Uncleaned version
3. Data Cleaning and Processing Functions
process_check_data(): Check for common errors in the
character dataset
process_check_data(
data = sauresia_morpho,
lat_col = "Latitude..decimal.",
long_col = "Longitude..decimal.",
elevation_col = "Elevation",
trait_columns = c(
"SVL", "pattern", "head.markings", "nuchal.lines",
"dots.in.lateral.band", "mental.to.vent.scale.count",
"midbody.scalecount", "total.finger.lamella", "strigae.on.ten.scales",
"total.toe.length", "scale.under.eye.to.lip.distance", "eye.length", "arm.length",
"ear.width", "rostral.width", "rostral.height", "head.length", "mental.width",
"post.mental.width", "cloaca.width", "prefrontal.width",
"largest.supraoccular.width", "Finger.III.length", "ear.to.eye.distance",
"head.width", "frontal.width", "frontal.lenght"),
date_col = "Date.Collected")
#> Notification-Inconsistent date formats were found, please check the date formats.
#>
#> No DMS coordinates found. :)
#>
#> Notification-Some coordinates are outside the valid range.
#> Latitude should be between -90 and 90, and Longitude should be between -180 and 180.
#>
#> Notification-Elevation ends with 'm' or 'meters'. This text needs to be removed.
#>
#> Notification-The following columns are not in the dataset: Institution, Region, Latitude, and Longitude. They are not required, but some functions may perform better if these columns exist in your dataset, even if they are left blank.
#>
#> No trait columns with more than 50% missing data. :)
#>
#> Notification-Character values detected in trait columns. These should be numeric.process_column_names(): Change column names to clean
versions
sauresia_morpho3 <- process_column_names(
sauresia_morpho2,
new_column_names = c(
"Name in Tree", "New names", "Type", "Genus", "Species", "Museum", "Number",
"Country", "Province", "Locality", "Elevation",
"Date Collected", "Collectors", "Remarks", "Latitude", "Longitude",
"SVL", "Pattern", "Head Markings", "Nuchal Lines", "Dots in Lateral Band",
"Mental to Vent Scale Count", "Midbody ScaleCount", "Total Finger Lamella",
"Strigae on Ten Scales", "Total Toe Length", "Scale Under Eye to Lip Distance",
"Eye Length", "Arm Length", "Ear Width", "Rostral Width", "Rostral Height",
"Head Length", "Mental Width", "Post Mental Width", "Cloaca Width",
"Prefrontal Width", "Largest Supraoccular Width", "Finger III Length",
"Ear to Eye Distance", "Head Width", "Frontal Width", "Frontal Length"))
#> Columns have been successfully renamed.process_juveniles(): Remove juviniles from the dataset
based on their trait size compared to the largest individual in their
respective group
process_juveniles(
sauresia_morpho3,
trait = "SVL",
group_by = "Species",
cutoff = 0.85)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `max_trait = max(SVL, na.rm = TRUE)`.
#> ℹ In group 9: `Species = "Wetmorena surda"`.
#> Caused by warning in `max()`:
#> ! no non-missing arguments to max; returning -Inf
#> $filtered_data
#> Name in Tree New names
#> 1 269778_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 1
#> 2 269901_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 4
#> 3 191850_Sauresia_sepsoides_HT_Pestel Sauresia cayemitae 1
#> 4 274050_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 2
#> 5 274211_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 4
#> 6 274224_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 6
#> 7 103643_Sauresia_gracilis_HT_Port_Salut Sauresia gracilis 1
#> 8 191913_Sauresia_pinguis_HT_Marche_Leon Sauresia habichi 1
#> 9 268585_Sauresia_manicula_HT_Berry Sauresia manicula 1
#> 10 268586_Sauresia_manicula_HT_Berry Sauresia manicula 2
#> 11 192312_Sauresia_pangnolae_HT_Baraderes Sauresia pangnolae 2
#> 12 274213_Sauresia_pangnolae_HT_Morne_Bois_Pangnol Sauresia pangnolae 4
#> 13 192469_Sauresia_sepsoides_DO_La_Zurza Sauresia sepsoides 4
#> 14 193040_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 5
#> 15 193041_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 6
#> 16 193201_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 11
#> 17 193202_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 12
#> 18 193203_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 13
#> 19 193204_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 14
#> 20 160343_Sauresia_synoria_DO_Pedernales Sauresia synoria 1
#> Type Genus Species Museum Number Country
#> 1 Paratype Sauresia Sauresia agramma ANSP 38685 Haiti
#> 2 Holotype Sauresia Sauresia agramma ANSP 38688
#> 3 Sauresia Sauresia cayemitae ANSP 38691 Haiti
#> 4 Sauresia Sauresia cayemitae ANSP 38673 Haiti
#> 5 Sauresia Sauresia cayemitae ANSP 38675 Haiti
#> 6 Sauresia Sauresia cayemitae ANSP 38676 Haiti
#> 7 Holotype Sauresia Sauresia gracilis UNSM 328852 Haiti
#> 8 Paratype Sauresia Sauresia habichi ANSP 38681 Haiti
#> 9 Holotype Sauresia Sauresia manicula ANSP 38667 Haiti
#> 10 Paratype Sauresia Sauresia manicula ANSP 38668 Haiti
#> 11 Paratype Sauresia Sauresia pangnolae ANSP 38663 Haiti
#> 12 Holotype Sauresia Sauresia pangnolae ANSP 38684 Haiti
#> 13 Paratype Sauresia Sauresia sepsoides ANSP 38678 Dominican Republic
#> 14 Paratype Sauresia Sauresia sepsoides ANSP 38670 Dominican Republic
#> 15 Paratype Sauresia Sauresia sepsoides ANSP 38671 Dominican Republic
#> 16 Paratype Sauresia Sauresia sepsoides ANSP 38706 Dominican Republic
#> 17 Paratype Sauresia Sauresia sepsoides ANSP 38707 Dominican Republic
#> 18 Paratype Sauresia Sauresia sepsoides ANSP 38708 Dominican Republic
#> 19 Paratype Sauresia Sauresia sepsoides ANSP 38709 Dominican Republic
#> 20 Paratype Sauresia Sauresia synoria SBH 160343 Dominican Republic
#> Province
#> 1 Sud-Est
#> 2
#> 3 Dept. de la Grand'Anse
#> 4 Grand'Anse
#> 5 Grand'Anse
#> 6 Grand'Anse
#> 7 Dept. du Sud
#> 8 Dept. de la Grand'Anse
#> 9 L'Ouest
#> 10 L'Ouest
#> 11 Dept. de la Grand'Anse
#> 12 Nippes
#> 13 La Altagracia
#> 14 Sanchez Ramirez Prov.
#> 15 Sanchez Ramirez Prov.
#> 16 Los Tabucos
#> 17 Los Tabucos
#> 18 Los Tabucos
#> 19 Los Tabucos
#> 20 Pedernales
#> Locality Elevation
#> 1 Morne D'Enfer 1433
#> 2 NA
#> 3 Pestel 5.0 km S of 300
#> 4 Grande Cayemite (helipad-camp) 74
#> 5 Grande Cayemite (waypoint 166) 38
#> 6 Grande Cayemite (waypoint 166) 38
#> 7 Port Salut 10.3 km NW 10
#> 8 Marche Leon 8.0 km S of 435
#> 9 Berry 1630
#> 10 Berry 1630
#> 11 Baraderes 8.0 km SSW of 420
#> 12 Morne Bois Pangnol 1170
#> 13 La Zanga 7.5 km W of (at Rio Maimon) 25
#> 14 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 15 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 16 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 17 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 18 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 19 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 20 Pedernales 22 km N at Rio Mulito 274
#> Date Collected
#> 1
#> 2
#> 3 5/25/1991
#> 4
#> 5
#> 6
#> 7 10/28/1984
#> 8 5/28/1991
#> 9
#> 10
#> 11 6/7/1991
#> 12
#> 13 7/20/1991
#> 14 7/11/1993
#> 15 7/11/1993
#> 16 7/21/1993
#> 17 7/21/1993
#> 18 7/21/1993
#> 19 7/21/1993
#> 20 6/22/1985
#> Collectors
#> 1
#> 2
#> 3 Richard Thomas and Manuel Leal
#> 4
#> 5
#> 6
#> 7 S. Blair Hedges and Richard Thomas
#> 8 S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer
#> 9
#> 10
#> 11 S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals
#> 12
#> 13 S. Blair Hedges Richard Thomas and Nicholas Plummer
#> 14 Manuel Leal Richard Thomas
#> 15 Manuel Leal Richard Thomas
#> 16 Richard Thomas
#> 17 Richard Thomas
#> 18 Richard Thomas
#> 19 Richard Thomas
#> 20 Richard Thomas and S. Blair Hedges
#> Remarks
#> 1
#> 2
#> 3 under rocks and logs
#> 4
#> 5
#> 6
#> 7 day; under objects and in leaf litter
#> 8
#> 9
#> 10
#> 11 eleuths found on limestone rocks A. cybotes and A. manticola found sleeping on ferns E. abbotti female found in leaf litter
#> 12
#> 13
#> 14 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 15 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 16 cacao-coffee grove
#> 17 cacao-coffee grove
#> 18 cacao-coffee grove
#> 19 cacao-coffee grove
#> 20 night; E inoptatus resting on leaf 6" high on stream bank; Epicrates striatus moving in a tree 5' above the stream; Sauresia under rock
#> Latitude Longitude SVL Pattern Head Markings Nuchal Lines
#> 1 18.33005 -72.37095 69.10 0 0 0
#> 2 NA NA 64.80 1 0 0
#> 3 18.51329 -73.78463 58.10 5 1 1
#> 4 18.63316 -73.75524 56.80 2 1 1
#> 5 18.63562 -73.75175 53.20 4 1 1
#> 6 18.63562 -73.75175 53.80 4 1 1
#> 7 18.14086 -73.96780 51.14 NA 1 1
#> 8 18.51678 -74.08311 59.70 3 1 1
#> 9 18.30795 -72.25389 69.00 3 NA 1
#> 10 18.30795 -72.25389 59.60 3 NA 1
#> 11 18.44032 -73.66756 66.70 1 0 1
#> 12 18.41869 -73.77512 66.10 1 0 0
#> 13 NA NA 62.80 2 0 0
#> 14 19.10370 -70.05310 62.80 2 0 0
#> 15 19.10370 -70.05310 59.10 1 0 0
#> 16 NA NA 65.20 2 0 1
#> 17 NA NA 59.60 1 0 0
#> 18 NA NA 58.90 1 0 0
#> 19 NA NA 59.00 2 1 1
#> 20 18.15440 -71.75810 63.66 0 1 1
#> Dots in Lateral Band Mental to Vent Scale Count Midbody ScaleCount
#> 1 0 123 38
#> 2 0 127 37
#> 3 0 117 37
#> 4 0 117 36
#> 5 0 115 33
#> 6 0 110 36
#> 7 0 103 36
#> 8 0 122 41
#> 9 0 129 37
#> 10 0 123 37
#> 11 1 113 39
#> 12 1 115 42
#> 13 0 118 36
#> 14 0 114 35
#> 15 0 117 37
#> 16 0 119 37
#> 17 0 118 36
#> 18 0 115 36
#> 19 0 114 36
#> 20 0 123 34
#> Total Finger Lamella Strigae on Ten Scales Total Toe Length
#> 1 17 103 7.80
#> 2 17 138 7.94
#> 3 19 84 7.80
#> 4 18 104 7.06
#> 5 18 93 7.13
#> 6 18 92 7.41
#> 7 18 100 7.07
#> 8 18 113 7.72
#> 9 17 150 8.32
#> 10 17 119 6.68
#> 11 19 109 8.82
#> 12 17 92 7.67
#> 13 17 101 7.70
#> 14 16 114 6.79
#> 15 16 96 6.35
#> 16 15 105 7.89
#> 17 17 97 7.14
#> 18 17 94 7.09
#> 19 17 106 7.86
#> 20 18 111 6.68
#> Scale Under Eye to Lip Distance Eye Length Arm Length Ear Width
#> 1 0.15 1.69 7.06 0.49
#> 2 0.17 1.49 7.14 0.43
#> 3 0.09 1.49 7.29 0.41
#> 4 0.13 1.57 6.58 0.46
#> 5 0.13 1.46 5.66 0.58
#> 6 0.03 1.55 6.34 0.63
#> 7 0.13 1.52 5.54 0.34
#> 8 0.12 1.38 7.04 0.38
#> 9 0.13 1.58 7.93 0.60
#> 10 0.10 1.38 7.09 0.36
#> 11 0.10 1.93 7.95 0.61
#> 12 0.12 1.69 7.54 0.45
#> 13 0.12 1.55 6.86 0.59
#> 14 0.19 1.57 5.95 0.50
#> 15 0.16 1.47 5.81 0.36
#> 16 0.14 1.62 6.41 0.40
#> 17 0.13 1.51 6.53 0.49
#> 18 0.16 1.47 6.27 0.30
#> 19 0.12 1.46 7.01 0.32
#> 20 0.20 1.57 5.82 0.39
#> Rostral Width Rostral Height Head Length Mental Width Post Mental Width
#> 1 1.55 0.76 9.42 1.11 1.62
#> 2 1.57 0.74 8.91 1.04 1.49
#> 3 1.41 0.75 8.02 0.85 1.42
#> 4 1.38 0.80 8.87 0.91 1.29
#> 5 1.19 0.72 7.20 0.77 1.24
#> 6 1.31 0.73 8.13 0.96 1.35
#> 7 1.33 0.70 8.03 0.90 1.41
#> 8 1.46 0.80 8.94 0.93 1.39
#> 9 1.73 0.91 9.83 1.15 1.49
#> 10 1.36 0.72 7.78 0.88 1.27
#> 11 1.94 0.94 10.10 1.27 1.65
#> 12 1.47 0.81 8.62 0.81 1.57
#> 13 1.72 0.90 9.28 1.09 1.42
#> 14 2.00 1.00 8.21 0.86 1.22
#> 15 1.50 0.81 7.87 0.97 1.29
#> 16 2.00 1.00 8.88 0.94 1.43
#> 17 1.53 0.74 8.44 0.91 1.25
#> 18 1.60 0.81 8.42 1.11 1.33
#> 19 1.60 0.66 9.11 0.87 1.27
#> 20 1.53 0.84 7.80 0.77 1.54
#> Cloaca Width Prefrontal Width Largest Supraoccular Width Finger III Length
#> 1 4.21 2.09 1.29 1.46
#> 2 3.96 2.16 1.23 1.49
#> 3 3.54 1.98 0.97 1.54
#> 4 3.53 2.01 1.20 1.40
#> 5 3.32 1.71 1.05 1.32
#> 6 3.31 1.88 1.07 1.28
#> 7 3.67 1.95 1.25 1.00
#> 8 3.99 2.25 1.33 1.40
#> 9 4.42 2.50 1.39 1.52
#> 10 3.16 1.98 1.11 1.32
#> 11 4.05 2.47 1.49 1.53
#> 12 4.20 NA 1.17 1.53
#> 13 3.87 2.36 1.31 1.33
#> 14 3.63 2.11 1.41 1.17
#> 15 3.78 2.09 1.12 1.03
#> 16 4.06 2.28 1.05 1.20
#> 17 3.48 1.98 1.11 1.28
#> 18 3.23 2.12 1.00 1.35
#> 19 3.63 2.31 1.28 1.38
#> 20 3.58 2.04 1.06 1.46
#> Ear to Eye Distance Head Width Frontal Width Frontal Length
#> 1 4.79 6.77 NA NA
#> 2 4.49 6.21 2.55 3.18
#> 3 3.87 5.91 2.06 2.82
#> 4 3.73 6.08 1.91 2.51
#> 5 3.26 5.55 1.87 2.33
#> 6 3.64 5.73 2.02 2.43
#> 7 3.90 5.43 2.03 2.45
#> 8 4.36 6.95 2.14 2.98
#> 9 5.17 8.14 2.55 3.13
#> 10 4.03 5.67 NA 2.59
#> 11 4.97 7.15 2.74 3.60
#> 12 4.59 6.74 2.06 2.96
#> 13 4.77 6.79 2.30 2.83
#> 14 3.85 5.88 2.35 2.79
#> 15 3.78 5.57 2.20 2.65
#> 16 4.20 6.43 2.25 2.92
#> 17 4.32 6.04 2.04 2.76
#> 18 4.03 5.89 2.08 2.87
#> 19 4.74 6.44 2.26 3.27
#> 20 3.76 5.93 NA 2.37
#>
#> $removed_summary
#> # A tibble: 9 × 2
#> Species removed
#> <chr> <int>
#> 1 Sauresia agramma 2
#> 2 Sauresia cayemitae 2
#> 3 Sauresia gracilis 0
#> 4 Sauresia habichi 1
#> 5 Sauresia manicula 0
#> 6 Sauresia pangnolae 2
#> 7 Sauresia sepsoides 4
#> 8 Sauresia synoria 0
#> 9 Wetmorena surda 0process_check_missing(): Check for the number and
proportion of missing values in each column
process_check_missing(data = sauresia_morpho3)
#> Column Missing_raw Missing_proportion
#> 1 Name in Tree 0 0.0000
#> 2 New names 0 0.0000
#> 3 Type 0 0.0000
#> 4 Genus 0 0.0000
#> 5 Species 0 0.0000
#> 6 Museum 0 0.0000
#> 7 Number 0 0.0000
#> 8 Country 0 0.0000
#> 9 Province 0 0.0000
#> 10 Locality 0 0.0000
#> 11 Elevation 6 0.1250
#> 12 Date Collected 0 0.0000
#> 13 Collectors 0 0.0000
#> 14 Remarks 0 0.0000
#> 15 Latitude 17 0.3542
#> 16 Longitude 17 0.3542
#> 17 SVL 17 0.3542
#> 18 Pattern 18 0.3750
#> 19 Head Markings 19 0.3958
#> 20 Nuchal Lines 17 0.3542
#> 21 Dots in Lateral Band 17 0.3542
#> 22 Mental to Vent Scale Count 18 0.3750
#> 23 Midbody ScaleCount 17 0.3542
#> 24 Total Finger Lamella 17 0.3542
#> 25 Strigae on Ten Scales 20 0.4167
#> 26 Total Toe Length 20 0.4167
#> 27 Scale Under Eye to Lip Distance 20 0.4167
#> 28 Eye Length 20 0.4167
#> 29 Arm Length 20 0.4167
#> 30 Ear Width 20 0.4167
#> 31 Rostral Width 20 0.4167
#> 32 Rostral Height 20 0.4167
#> 33 Head Length 19 0.3958
#> 34 Mental Width 20 0.4167
#> 35 Post Mental Width 20 0.4167
#> 36 Cloaca Width 20 0.4167
#> 37 Prefrontal Width 21 0.4375
#> 38 Largest Supraoccular Width 20 0.4167
#> 39 Finger III Length 20 0.4167
#> 40 Ear to Eye Distance 20 0.4167
#> 41 Head Width 20 0.4167
#> 42 Frontal Width 23 0.4792
#> 43 Frontal Length 21 0.4375process_convert_units(): Convert the units of specified
traits
process_convert_units(
data = sauresia_morpho3,
trait_column = "SVL",
conversion_factor = 10)
#> Name in Tree New names
#> 1 269778_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 1
#> 2 269899_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 2
#> 3 269900_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 3
#> 4 269901_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 4
#> 5 191850_Sauresia_sepsoides_HT_Pestel Sauresia cayemitae 1
#> 6 274050_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 2
#> 7 274113_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 3
#> 8 274211_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 4
#> 9 274212_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 5
#> 10 274224_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 6
#> 11 103643_Sauresia_gracilis_HT_Port_Salut Sauresia gracilis 1
#> 12 191913_Sauresia_pinguis_HT_Marche_Leon Sauresia habichi 1
#> 13 191915_Sauresia_pinguis_HT_Marche_Leon Sauresia habichi 2
#> 14 268585_Sauresia_manicula_HT_Berry Sauresia manicula 1
#> 15 268586_Sauresia_manicula_HT_Berry Sauresia manicula 2
#> 16 191851_Sauresia_pangnolae_HT_Pestel Sauresia pangnolae 1
#> 17 192312_Sauresia_pangnolae_HT_Baraderes Sauresia pangnolae 2
#> 18 192313_Sauresia_pangnolae_HT_Baraderes Sauresia pangnolae 3
#> 19 274213_Sauresia_pangnolae_HT_Morne_Bois_Pangnol Sauresia pangnolae 4
#> 20 102369_Sauresia_sepsoides_DO_Sabana_de_la_Mar Sauresia sepsoides 1
#> 21 102383_Sauresia_sepsoides_DO_El_Valle Sauresia sepsoides 2
#> 22 102384_Sauresia_sepsoides_DO_El_Valle Sauresia sepsoides 3
#> 23 192469_Sauresia_sepsoides_DO_La_Zurza Sauresia sepsoides 4
#> 24 193040_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 5
#> 25 193041_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 6
#> 26 193042_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 7
#> 27 193093_Sauresia_sepsoides_DO_Batez_Piedra Sauresia sepsoides 8
#> 28 193116_Sauresia_sepsoides_DO_Majagual Sauresia sepsoides 9
#> 29 193149_Sauresia_sepsoides_DO_Loma_Quita_Espuela Sauresia sepsoides 10
#> 30 193201_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 11
#> 31 193202_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 12
#> 32 193203_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 13
#> 33 193204_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 14
#> 34 266746_Sauresia_sepsoides_DO_Los_Limones Sauresia sepsoides 15
#> 35 266748_Sauresia_sepsoides_HT_Jacmel Sauresia sepsoides 16
#> 36 266749_Sauresia_sepsoides_HT_Jacmel Sauresia sepsoides 17
#> 37 266750_Sauresia_sepsoides_DO_Los_Limones Sauresia sepsoides 18
#> 38 266754_Sauresia_sepsoides_DO_S_Los_Limones Sauresia sepsoides 19
#> 39 267754_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 20
#> 40 267755_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 21
#> 41 267756_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 22
#> 42 267757_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 23
#> 43 267758_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 24
#> 44 267773_Sauresia_sepsoides_DO_1765_W_El_Valle Sauresia sepsoides 25
#> 45 267780_Sauresia_sepsoides_DO_1766_S_Naranjo_Arriba Sauresia sepsoides 26
#> 46 267781_Sauresia_sepsoides_DO_1766_S_Naranjo_Arriba Sauresia sepsoides 27
#> 47 160343_Sauresia_synoria_DO_Pedernales Sauresia synoria 1
#> 48 266705_Wetmorena_haetiana_surda_DO_N_Los_Arroyos Wetmorena surda 1
#> Type Genus Species Museum Number Country
#> 1 Paratype Sauresia Sauresia agramma ANSP 38685 Haiti
#> 2 Paratype Sauresia Sauresia agramma ANSP 38686
#> 3 Paratype Sauresia Sauresia agramma ANSP 38687
#> 4 Holotype Sauresia Sauresia agramma ANSP 38688
#> 5 Sauresia Sauresia cayemitae ANSP 38691 Haiti
#> 6 Sauresia Sauresia cayemitae ANSP 38673 Haiti
#> 7 Sauresia Sauresia cayemitae ANSP 38674 Haiti
#> 8 Sauresia Sauresia cayemitae ANSP 38675 Haiti
#> 9 Paratype Sauresia Sauresia cayemitae SBH 274212 Haiti
#> 10 Sauresia Sauresia cayemitae ANSP 38676 Haiti
#> 11 Holotype Sauresia Sauresia gracilis UNSM 328852 Haiti
#> 12 Paratype Sauresia Sauresia habichi ANSP 38681 Haiti
#> 13 Holotype Sauresia Sauresia habichi ANSP 38683 Haiti
#> 14 Holotype Sauresia Sauresia manicula ANSP 38667 Haiti
#> 15 Paratype Sauresia Sauresia manicula ANSP 38668 Haiti
#> 16 Paratype Sauresia Sauresia pangnolae ANSP 38690 Haiti
#> 17 Paratype Sauresia Sauresia pangnolae ANSP 38663 Haiti
#> 18 Paratype Sauresia Sauresia pangnolae ANSP 38664 Haiti
#> 19 Holotype Sauresia Sauresia pangnolae ANSP 38684 Haiti
#> 20 Sauresia Sauresia sepsoides UNSM 328846 Dominican Republic
#> 21 Sauresia Sauresia sepsoides UNSM 328850 Dominican Republic
#> 22 Sauresia Sauresia sepsoides UNSM 328851 Dominican Republic
#> 23 Paratype Sauresia Sauresia sepsoides ANSP 38678 Dominican Republic
#> 24 Paratype Sauresia Sauresia sepsoides ANSP 38670 Dominican Republic
#> 25 Paratype Sauresia Sauresia sepsoides ANSP 38671 Dominican Republic
#> 26 Paratype Sauresia Sauresia sepsoides ANSP 38672 Dominican Republic
#> 27 Paratype Sauresia Sauresia sepsoides ANSP 38666 Dominican Republic
#> 28 Paratype Sauresia Sauresia sepsoides ANSP 38680 Dominican Republic
#> 29 Sauresia Sauresia sepsoides SBH 193149 Dominican Republic
#> 30 Paratype Sauresia Sauresia sepsoides ANSP 38706 Dominican Republic
#> 31 Paratype Sauresia Sauresia sepsoides ANSP 38707 Dominican Republic
#> 32 Paratype Sauresia Sauresia sepsoides ANSP 38708 Dominican Republic
#> 33 Paratype Sauresia Sauresia sepsoides ANSP 38709 Dominican Republic
#> 34 Sauresia Sauresia sepsoides SBH 266746 Dominican Republic
#> 35 Sauresia Sauresia sepsoides SBH 266748 Dominican Republic
#> 36 Sauresia Sauresia sepsoides SBH 266749 Dominican Republic
#> 37 Sauresia Sauresia sepsoides SBH 266750 Dominican Republic
#> 38 Sauresia Sauresia sepsoides SBH 266754 Dominican Republic
#> 39 Sauresia Sauresia sepsoides SBH 267754 Dominican Republic
#> 40 Sauresia Sauresia sepsoides SBH 267755 Dominican Republic
#> 41 Sauresia Sauresia sepsoides SBH 267756 Dominican Republic
#> 42 Sauresia Sauresia sepsoides SBH 267757 Dominican Republic
#> 43 Sauresia Sauresia sepsoides SBH 267758 Dominican Republic
#> 44 Sauresia Sauresia sepsoides SBH 267773 Dominican Republic
#> 45 Sauresia Sauresia sepsoides SBH 267780 Dominican Republic
#> 46 Sauresia Sauresia sepsoides SBH 267781 Dominican Republic
#> 47 Paratype Sauresia Sauresia synoria SBH 160343 Dominican Republic
#> 48 Wetmorena Wetmorena surda SBH 266705 Dominican Republic
#> Province
#> 1 Sud-Est
#> 2
#> 3
#> 4
#> 5 Dept. de la Grand'Anse
#> 6 Grand'Anse
#> 7 Grand'Anse
#> 8 Grand'Anse
#> 9 Grand'Anse
#> 10 Grand'Anse
#> 11 Dept. du Sud
#> 12 Dept. de la Grand'Anse
#> 13 Dept. de la Grand'Anse
#> 14 L'Ouest
#> 15 L'Ouest
#> 16 Dept. de la Grand'Anse
#> 17 Dept. de la Grand'Anse
#> 18 Dept. de la Grand'Anse
#> 19 Nippes
#> 20 Hato Mayor
#> 21 Hato Mayor
#> 22 Hato Mayor
#> 23 La Altagracia
#> 24 Sanchez Ramirez Prov.
#> 25 Sanchez Ramirez Prov.
#> 26 Sanchez Ramirez Prov.
#> 27 Duarte Prov.
#> 28 Monte Plata Prov.
#> 29 Duarte Prov.
#> 30 Los Tabucos
#> 31 Los Tabucos
#> 32 Los Tabucos
#> 33 Los Tabucos
#> 34 Monte Plata
#> 35 Monte Plata
#> 36 Monte Plata
#> 37 Monte Plata
#> 38 Monte Plata
#> 39 Monte Plata
#> 40 Monte Plata
#> 41 Monte Plata
#> 42 Monte Plata
#> 43 Monte Plata
#> 44 Hato Mayor
#> 45 Parque Nacional Los Haitises
#> 46 Parque Nacional Los Haitises
#> 47 Pedernales
#> 48 Pedernales
#> Locality Elevation
#> 1 Morne D'Enfer 1433
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 Pestel 5.0 km S of 300
#> 6 Grande Cayemite (helipad-camp) 74
#> 7 Grande Cayemite (waypoint 166) 38
#> 8 Grande Cayemite (waypoint 166) 38
#> 9 Grande Cayemite (waypoint 166) 38
#> 10 Grande Cayemite (waypoint 166) 38
#> 11 Port Salut 10.3 km NW 10
#> 12 Marche Leon 8.0 km S of 435
#> 13 Marche Leon 8.0 km S of 435
#> 14 Berry 1630
#> 15 Berry 1630
#> 16 Pestel 11.8 km S of 550
#> 17 Baraderes 8.0 km SSW of 420
#> 18 Baraderes 8.0 km SSW of 420
#> 19 Morne Bois Pangnol 1170
#> 20 Sabana De La Mar 9.5 km W (airline) in Los Haitises NA
#> 21 El Valle ca 15 km W (on road to Trepada Alta) NA
#> 22 El Valle ca 15 km W (on road to Trepada Alta) NA
#> 23 La Zanga 7.5 km W of (at Rio Maimon) 25
#> 24 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 25 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 26 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 27 Batez Piedra on west side of Rio Pazabo 35
#> 28 Majagual 4.3 km N of 90
#> 29 Southern slopes of Loma Quita Espuela 775
#> 30 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 31 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 32 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 33 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 34 Los Limones footpath N of town 197
#> 35 Los Limones 3km S 275
#> 36 Los Limones 3km S 275
#> 37 Los Limones 3km S 275
#> 38 6km S Los Limones 305
#> 39 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 40 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 41 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 42 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 43 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 44 14.1 km W El Valle; Lat: 19d0.393' N Long: 69d29.333' W 193
#> 45 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W 150
#> 46 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W 150
#> 47 Pedernales 22 km N at Rio Mulito 274
#> 48 N Los Arroyos 1660
#> Date Collected
#> 1
#> 2
#> 3
#> 4
#> 5 5/25/1991
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 10/28/1984
#> 12 5/28/1991
#> 13 5/28/1991
#> 14
#> 15
#> 16 5/25/1991
#> 17 6/7/1991
#> 18 6/7/1991
#> 19
#> 20 8/11/1984
#> 21 8/10/1984
#> 22 8/10/1984
#> 23 7/20/1991
#> 24 7/11/1993
#> 25 7/11/1993
#> 26 7/11/1993
#> 27 7/13/1993
#> 28 7/13/1993
#> 29 7/16/1993
#> 30 7/21/1993
#> 31 7/21/1993
#> 32 7/21/1993
#> 33 7/21/1993
#> 34 3/27/2004
#> 35 3/26/2004
#> 36 3/26/2004
#> 37 3/26/2004
#> 38 3/26/2004
#> 39 7/7/2006
#> 40 7/7/2006
#> 41 7/7/2006
#> 42 7/7/2006
#> 43 7/7/2006
#> 44
#> 45
#> 46
#> 47 6/22/1985
#> 48 3/23/2004
#> Collectors
#> 1
#> 2
#> 3
#> 4
#> 5 Richard Thomas and Manuel Leal
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 S. Blair Hedges and Richard Thomas
#> 12 S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer
#> 13 S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer
#> 14
#> 15
#> 16 Richard Thomas and Manuel Leal
#> 17 S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals
#> 18 S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals
#> 19
#> 20 S. Blair Hedges and Richard Thomas
#> 21 S. Blair Hedges and Richard Thomas
#> 22 S. Blair Hedges and Richard Thomas
#> 23 S. Blair Hedges Richard Thomas and Nicholas Plummer
#> 24 Manuel Leal Richard Thomas
#> 25 Manuel Leal Richard Thomas
#> 26 Manuel Leal Richard Thomas
#> 27 Richard Thomas Manuel Leal and Herman Dominicia
#> 28 Richard Thomas
#> 29 Herman Dominicia Richard Thomas
#> 30 Richard Thomas
#> 31 Richard Thomas
#> 32 Richard Thomas
#> 33 Richard Thomas
#> 34 Richard Thomas
#> 35 Richard Thomas
#> 36 Richard Thomas
#> 37 Richard Thomas
#> 38 Richard Thomas
#> 39 RT
#> 40 RT
#> 41 RT
#> 42 RT
#> 43 RT
#> 44 RT EF and SBH
#> 45
#> 46
#> 47 Richard Thomas and S. Blair Hedges
#> 48
#> Remarks
#> 1
#> 2
#> 3
#> 4
#> 5 under rocks and logs
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 day; under objects and in leaf litter
#> 12
#> 13
#> 14
#> 15
#> 16
#> 17 eleuths found on limestone rocks A. cybotes and A. manticola found sleeping on ferns E. abbotti female found in leaf litter
#> 18 eleuths found on limestone rocks A. cybotes and A. manticola found sleeping on ferns E. abbotti female found in leaf litter
#> 19
#> 20 day; all under rocks along a dry slope ca. 1 mile SE of base camp (C-159) by trail (not straight)
#> 21 under rocks and logs in pasture limestone outcrops nearby; day
#> 22 under rocks and logs in pasture limestone outcrops nearby; day
#> 23
#> 24 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 25 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 26 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 27 locality = ca. 10.5 km airline NNE of Cervicos
#> 28 coffee grove in the Haitises; some rocks but not a lot and some rotten logs
#> 29
#> 30 cacao-coffee grove
#> 31 cacao-coffee grove
#> 32 cacao-coffee grove
#> 33 cacao-coffee grove
#> 34
#> 35
#> 36
#> 37
#> 38
#> 39
#> 40
#> 41
#> 42
#> 43
#> 44
#> 45
#> 46
#> 47 night; E inoptatus resting on leaf 6" high on stream bank; Epicrates striatus moving in a tree 5' above the stream; Sauresia under rock
#> 48
#> Latitude Longitude SVL Pattern Head Markings Nuchal Lines
#> 1 18.33005 -72.37095 69.10 0 0 0
#> 2 NA NA 53.80 1 1 0
#> 3 NA NA 49.40 0 0 0
#> 4 NA NA 64.80 1 0 0
#> 5 18.51329 -73.78463 58.10 5 1 1
#> 6 18.63316 -73.75524 56.80 2 1 1
#> 7 18.63562 -73.75175 47.80 4 1 1
#> 8 18.63562 -73.75175 53.20 4 1 1
#> 9 18.63562 -73.75175 49.37 5 1 1
#> 10 18.63562 -73.75175 53.80 4 1 1
#> 11 18.14086 -73.96780 51.14 NA 1 1
#> 12 18.51678 -74.08311 59.70 3 1 1
#> 13 18.51678 -74.08311 50.50 5 1 1
#> 14 18.30795 -72.25389 69.00 3 NA 1
#> 15 18.30795 -72.25389 59.60 3 NA 1
#> 16 18.47942 -73.78744 54.30 2 0 0
#> 17 18.44032 -73.66756 66.70 1 0 1
#> 18 18.44032 -73.66756 54.30 1 0 1
#> 19 18.41869 -73.77512 66.10 1 0 0
#> 20 19.05293 -69.47899 NA NA NA NA
#> 21 NA NA NA NA NA NA
#> 22 NA NA NA NA NA NA
#> 23 NA NA 62.80 2 0 0
#> 24 19.10370 -70.05310 62.80 2 0 0
#> 25 19.10370 -70.05310 59.10 1 0 0
#> 26 19.10370 -70.05310 54.80 2 1 0
#> 27 19.06997 -69.90815 48.60 1 0 0
#> 28 19.07539 -69.82842 54.60 2 1 0
#> 29 NA NA 32.75 2 1 1
#> 30 NA NA 65.20 2 0 1
#> 31 NA NA 59.60 1 0 0
#> 32 NA NA 58.90 1 0 0
#> 33 NA NA 59.00 2 1 1
#> 34 NA NA NA NA NA NA
#> 35 NA NA NA NA NA NA
#> 36 NA NA NA NA NA NA
#> 37 NA NA NA NA NA NA
#> 38 NA NA NA NA NA NA
#> 39 19.01932 -69.73766 NA NA NA NA
#> 40 19.01932 -69.73766 NA NA NA NA
#> 41 19.01932 -69.73766 NA NA NA NA
#> 42 19.01932 -69.73766 NA NA NA NA
#> 43 19.01932 -69.73766 NA NA NA NA
#> 44 NA NA NA NA NA NA
#> 45 19.06667 -69.57127 NA NA NA NA
#> 46 19.06667 -69.57127 NA NA NA NA
#> 47 18.15440 -71.75810 63.66 0 1 1
#> 48 18.25790 -71.74460 NA NA NA NA
#> Dots in Lateral Band Mental to Vent Scale Count Midbody ScaleCount
#> 1 0 123 38
#> 2 0 121 39
#> 3 0 124 37
#> 4 0 127 37
#> 5 0 117 37
#> 6 0 117 36
#> 7 0 111 32
#> 8 0 115 33
#> 9 0 NA 34
#> 10 0 110 36
#> 11 0 103 36
#> 12 0 122 41
#> 13 0 125 38
#> 14 0 129 37
#> 15 0 123 37
#> 16 1 109 38
#> 17 1 113 39
#> 18 1 104 39
#> 19 1 115 42
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 0 118 36
#> 24 0 114 35
#> 25 0 117 37
#> 26 0 111 37
#> 27 0 116 36
#> 28 0 108 36
#> 29 0 116 36
#> 30 0 119 37
#> 31 0 118 36
#> 32 0 115 36
#> 33 0 114 36
#> 34 NA NA NA
#> 35 NA NA NA
#> 36 NA NA NA
#> 37 NA NA NA
#> 38 NA NA NA
#> 39 NA NA NA
#> 40 NA NA NA
#> 41 NA NA NA
#> 42 NA NA NA
#> 43 NA NA NA
#> 44 NA NA NA
#> 45 NA NA NA
#> 46 NA NA NA
#> 47 0 123 34
#> 48 NA NA NA
#> Total Finger Lamella Strigae on Ten Scales Total Toe Length
#> 1 17 103 7.80
#> 2 17 103 8.04
#> 3 17 NA NA
#> 4 17 138 7.94
#> 5 19 84 7.80
#> 6 18 104 7.06
#> 7 19 94 6.71
#> 8 18 93 7.13
#> 9 16 89 5.69
#> 10 18 92 7.41
#> 11 18 100 7.07
#> 12 18 113 7.72
#> 13 19 89 6.63
#> 14 17 150 8.32
#> 15 17 119 6.68
#> 16 15 96 7.42
#> 17 19 109 8.82
#> 18 18 104 7.77
#> 19 17 92 7.67
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 17 101 7.70
#> 24 16 114 6.79
#> 25 16 96 6.35
#> 26 17 97 6.41
#> 27 16 NA NA
#> 28 17 104 8.24
#> 29 14 NA NA
#> 30 15 105 7.89
#> 31 17 97 7.14
#> 32 17 94 7.09
#> 33 17 106 7.86
#> 34 NA NA NA
#> 35 NA NA NA
#> 36 NA NA NA
#> 37 NA NA NA
#> 38 NA NA NA
#> 39 NA NA NA
#> 40 NA NA NA
#> 41 NA NA NA
#> 42 NA NA NA
#> 43 NA NA NA
#> 44 NA NA NA
#> 45 NA NA NA
#> 46 NA NA NA
#> 47 18 111 6.68
#> 48 NA NA NA
#> Scale Under Eye to Lip Distance Eye Length Arm Length Ear Width
#> 1 0.15 1.69 7.06 0.49
#> 2 0.14 1.70 7.31 0.31
#> 3 NA NA NA NA
#> 4 0.17 1.49 7.14 0.43
#> 5 0.09 1.49 7.29 0.41
#> 6 0.13 1.57 6.58 0.46
#> 7 0.06 1.27 5.49 0.50
#> 8 0.13 1.46 5.66 0.58
#> 9 0.14 1.29 5.57 0.55
#> 10 0.03 1.55 6.34 0.63
#> 11 0.13 1.52 5.54 0.34
#> 12 0.12 1.38 7.04 0.38
#> 13 0.03 1.21 6.61 0.34
#> 14 0.13 1.58 7.93 0.60
#> 15 0.10 1.38 7.09 0.36
#> 16 0.08 1.64 6.84 0.44
#> 17 0.10 1.93 7.95 0.61
#> 18 0.07 1.51 6.78 0.60
#> 19 0.12 1.69 7.54 0.45
#> 20 NA NA NA NA
#> 21 NA NA NA NA
#> 22 NA NA NA NA
#> 23 0.12 1.55 6.86 0.59
#> 24 0.19 1.57 5.95 0.50
#> 25 0.16 1.47 5.81 0.36
#> 26 0.15 1.49 6.20 0.37
#> 27 NA NA NA NA
#> 28 0.11 1.36 6.81 0.54
#> 29 NA NA NA NA
#> 30 0.14 1.62 6.41 0.40
#> 31 0.13 1.51 6.53 0.49
#> 32 0.16 1.47 6.27 0.30
#> 33 0.12 1.46 7.01 0.32
#> 34 NA NA NA NA
#> 35 NA NA NA NA
#> 36 NA NA NA NA
#> 37 NA NA NA NA
#> 38 NA NA NA NA
#> 39 NA NA NA NA
#> 40 NA NA NA NA
#> 41 NA NA NA NA
#> 42 NA NA NA NA
#> 43 NA NA NA NA
#> 44 NA NA NA NA
#> 45 NA NA NA NA
#> 46 NA NA NA NA
#> 47 0.20 1.57 5.82 0.39
#> 48 NA NA NA NA
#> Rostral Width Rostral Height Head Length Mental Width Post Mental Width
#> 1 1.55 0.76 9.42 1.11 1.62
#> 2 1.50 0.78 8.20 1.10 1.45
#> 3 NA NA NA NA NA
#> 4 1.57 0.74 8.91 1.04 1.49
#> 5 1.41 0.75 8.02 0.85 1.42
#> 6 1.38 0.80 8.87 0.91 1.29
#> 7 1.16 0.53 7.02 0.83 1.15
#> 8 1.19 0.72 7.20 0.77 1.24
#> 9 1.39 0.51 6.61 0.82 1.23
#> 10 1.31 0.73 8.13 0.96 1.35
#> 11 1.33 0.70 8.03 0.90 1.41
#> 12 1.46 0.80 8.94 0.93 1.39
#> 13 1.43 0.59 7.16 0.92 1.18
#> 14 1.73 0.91 9.83 1.15 1.49
#> 15 1.36 0.72 7.78 0.88 1.27
#> 16 1.38 0.80 8.34 0.79 1.11
#> 17 1.94 0.94 10.10 1.27 1.65
#> 18 1.39 0.76 8.30 0.95 1.31
#> 19 1.47 0.81 8.62 0.81 1.57
#> 20 NA NA NA NA NA
#> 21 NA NA NA NA NA
#> 22 NA NA NA NA NA
#> 23 1.72 0.90 9.28 1.09 1.42
#> 24 2.00 1.00 8.21 0.86 1.22
#> 25 1.50 0.81 7.87 0.97 1.29
#> 26 1.46 0.95 8.04 0.89 1.12
#> 27 NA NA 7.34 NA NA
#> 28 1.45 0.75 8.13 0.78 1.18
#> 29 NA NA NA NA NA
#> 30 2.00 1.00 8.88 0.94 1.43
#> 31 1.53 0.74 8.44 0.91 1.25
#> 32 1.60 0.81 8.42 1.11 1.33
#> 33 1.60 0.66 9.11 0.87 1.27
#> 34 NA NA NA NA NA
#> 35 NA NA NA NA NA
#> 36 NA NA NA NA NA
#> 37 NA NA NA NA NA
#> 38 NA NA NA NA NA
#> 39 NA NA NA NA NA
#> 40 NA NA NA NA NA
#> 41 NA NA NA NA NA
#> 42 NA NA NA NA NA
#> 43 NA NA NA NA NA
#> 44 NA NA NA NA NA
#> 45 NA NA NA NA NA
#> 46 NA NA NA NA NA
#> 47 1.53 0.84 7.80 0.77 1.54
#> 48 NA NA NA NA NA
#> Cloaca Width Prefrontal Width Largest Supraoccular Width Finger III Length
#> 1 4.21 2.09 1.29 1.46
#> 2 3.67 2.14 1.33 1.54
#> 3 NA NA NA NA
#> 4 3.96 2.16 1.23 1.49
#> 5 3.54 1.98 0.97 1.54
#> 6 3.53 2.01 1.20 1.40
#> 7 2.67 1.74 1.04 1.25
#> 8 3.32 1.71 1.05 1.32
#> 9 3.03 1.66 1.11 1.13
#> 10 3.31 1.88 1.07 1.28
#> 11 3.67 1.95 1.25 1.00
#> 12 3.99 2.25 1.33 1.40
#> 13 3.07 2.00 1.05 1.37
#> 14 4.42 2.50 1.39 1.52
#> 15 3.16 1.98 1.11 1.32
#> 16 3.70 2.01 1.15 1.38
#> 17 4.05 2.47 1.49 1.53
#> 18 3.66 2.08 1.43 1.38
#> 19 4.20 NA 1.17 1.53
#> 20 NA NA NA NA
#> 21 NA NA NA NA
#> 22 NA NA NA NA
#> 23 3.87 2.36 1.31 1.33
#> 24 3.63 2.11 1.41 1.17
#> 25 3.78 2.09 1.12 1.03
#> 26 3.01 2.03 1.01 1.20
#> 27 NA NA NA NA
#> 28 3.37 2.05 1.06 1.23
#> 29 NA NA NA NA
#> 30 4.06 2.28 1.05 1.20
#> 31 3.48 1.98 1.11 1.28
#> 32 3.23 2.12 1.00 1.35
#> 33 3.63 2.31 1.28 1.38
#> 34 NA NA NA NA
#> 35 NA NA NA NA
#> 36 NA NA NA NA
#> 37 NA NA NA NA
#> 38 NA NA NA NA
#> 39 NA NA NA NA
#> 40 NA NA NA NA
#> 41 NA NA NA NA
#> 42 NA NA NA NA
#> 43 NA NA NA NA
#> 44 NA NA NA NA
#> 45 NA NA NA NA
#> 46 NA NA NA NA
#> 47 3.58 2.04 1.06 1.46
#> 48 NA NA NA NA
#> Ear to Eye Distance Head Width Frontal Width Frontal Length SVL_converted_10
#> 1 4.79 6.77 NA NA 691.0
#> 2 4.23 6.12 2.31 2.82 538.0
#> 3 NA NA NA NA 494.0
#> 4 4.49 6.21 2.55 3.18 648.0
#> 5 3.87 5.91 2.06 2.82 581.0
#> 6 3.73 6.08 1.91 2.51 568.0
#> 7 3.29 5.21 1.79 2.36 478.0
#> 8 3.26 5.55 1.87 2.33 532.0
#> 9 2.97 5.02 1.63 2.23 493.7
#> 10 3.64 5.73 2.02 2.43 538.0
#> 11 3.90 5.43 2.03 2.45 511.4
#> 12 4.36 6.95 2.14 2.98 597.0
#> 13 3.41 5.63 1.88 2.54 505.0
#> 14 5.17 8.14 2.55 3.13 690.0
#> 15 4.03 5.67 NA 2.59 596.0
#> 16 4.04 6.24 2.12 2.60 543.0
#> 17 4.97 7.15 2.74 3.60 667.0
#> 18 4.05 6.49 2.11 2.76 543.0
#> 19 4.59 6.74 2.06 2.96 661.0
#> 20 NA NA NA NA NA
#> 21 NA NA NA NA NA
#> 22 NA NA NA NA NA
#> 23 4.77 6.79 2.30 2.83 628.0
#> 24 3.85 5.88 2.35 2.79 628.0
#> 25 3.78 5.57 2.20 2.65 591.0
#> 26 3.75 5.20 2.12 2.57 548.0
#> 27 NA NA NA NA 486.0
#> 28 3.77 5.59 2.06 2.72 546.0
#> 29 NA NA NA NA 327.5
#> 30 4.20 6.43 2.25 2.92 652.0
#> 31 4.32 6.04 2.04 2.76 596.0
#> 32 4.03 5.89 2.08 2.87 589.0
#> 33 4.74 6.44 2.26 3.27 590.0
#> 34 NA NA NA NA NA
#> 35 NA NA NA NA NA
#> 36 NA NA NA NA NA
#> 37 NA NA NA NA NA
#> 38 NA NA NA NA NA
#> 39 NA NA NA NA NA
#> 40 NA NA NA NA NA
#> 41 NA NA NA NA NA
#> 42 NA NA NA NA NA
#> 43 NA NA NA NA NA
#> 44 NA NA NA NA NA
#> 45 NA NA NA NA NA
#> 46 NA NA NA NA NA
#> 47 3.76 5.93 NA 2.37 636.6
#> 48 NA NA NA NA NAprocess_standardize_traits(): Standardize traits by a
reference trait
process_standardize_traits(
data = sauresia_morpho3,
reference_trait = "SVL",
traits_to_standardize = c(
"SVL",
"Pattern",
"Head Markings",
"Head Width", "Frontal Width"))
#> Name in Tree New names
#> 1 269778_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 1
#> 2 269899_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 2
#> 3 269900_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 3
#> 4 269901_Sauresia_agramma_HT_Morne_d_Enfer Sauresia agramma 4
#> 5 191850_Sauresia_sepsoides_HT_Pestel Sauresia cayemitae 1
#> 6 274050_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 2
#> 7 274113_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 3
#> 8 274211_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 4
#> 9 274212_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 5
#> 10 274224_Sauresia_cayemitae_HT_Grande_Cayemite Sauresia cayemitae 6
#> 11 103643_Sauresia_gracilis_HT_Port_Salut Sauresia gracilis 1
#> 12 191913_Sauresia_pinguis_HT_Marche_Leon Sauresia habichi 1
#> 13 191915_Sauresia_pinguis_HT_Marche_Leon Sauresia habichi 2
#> 14 268585_Sauresia_manicula_HT_Berry Sauresia manicula 1
#> 15 268586_Sauresia_manicula_HT_Berry Sauresia manicula 2
#> 16 191851_Sauresia_pangnolae_HT_Pestel Sauresia pangnolae 1
#> 17 192312_Sauresia_pangnolae_HT_Baraderes Sauresia pangnolae 2
#> 18 192313_Sauresia_pangnolae_HT_Baraderes Sauresia pangnolae 3
#> 19 274213_Sauresia_pangnolae_HT_Morne_Bois_Pangnol Sauresia pangnolae 4
#> 20 102369_Sauresia_sepsoides_DO_Sabana_de_la_Mar Sauresia sepsoides 1
#> 21 102383_Sauresia_sepsoides_DO_El_Valle Sauresia sepsoides 2
#> 22 102384_Sauresia_sepsoides_DO_El_Valle Sauresia sepsoides 3
#> 23 192469_Sauresia_sepsoides_DO_La_Zurza Sauresia sepsoides 4
#> 24 193040_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 5
#> 25 193041_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 6
#> 26 193042_Sauresia_sepsoides_DO_Cotui Sauresia sepsoides 7
#> 27 193093_Sauresia_sepsoides_DO_Batez_Piedra Sauresia sepsoides 8
#> 28 193116_Sauresia_sepsoides_DO_Majagual Sauresia sepsoides 9
#> 29 193149_Sauresia_sepsoides_DO_Loma_Quita_Espuela Sauresia sepsoides 10
#> 30 193201_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 11
#> 31 193202_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 12
#> 32 193203_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 13
#> 33 193204_Sauresia_sepsoides_DO_Tenares Sauresia sepsoides 14
#> 34 266746_Sauresia_sepsoides_DO_Los_Limones Sauresia sepsoides 15
#> 35 266748_Sauresia_sepsoides_HT_Jacmel Sauresia sepsoides 16
#> 36 266749_Sauresia_sepsoides_HT_Jacmel Sauresia sepsoides 17
#> 37 266750_Sauresia_sepsoides_DO_Los_Limones Sauresia sepsoides 18
#> 38 266754_Sauresia_sepsoides_DO_S_Los_Limones Sauresia sepsoides 19
#> 39 267754_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 20
#> 40 267755_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 21
#> 41 267756_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 22
#> 42 267757_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 23
#> 43 267758_Sauresia_sepsoides_DO_1769_SW_Los_Limones Sauresia sepsoides 24
#> 44 267773_Sauresia_sepsoides_DO_1765_W_El_Valle Sauresia sepsoides 25
#> 45 267780_Sauresia_sepsoides_DO_1766_S_Naranjo_Arriba Sauresia sepsoides 26
#> 46 267781_Sauresia_sepsoides_DO_1766_S_Naranjo_Arriba Sauresia sepsoides 27
#> 47 160343_Sauresia_synoria_DO_Pedernales Sauresia synoria 1
#> 48 266705_Wetmorena_haetiana_surda_DO_N_Los_Arroyos Wetmorena surda 1
#> Type Genus Species Museum Number Country
#> 1 Paratype Sauresia Sauresia agramma ANSP 38685 Haiti
#> 2 Paratype Sauresia Sauresia agramma ANSP 38686
#> 3 Paratype Sauresia Sauresia agramma ANSP 38687
#> 4 Holotype Sauresia Sauresia agramma ANSP 38688
#> 5 Sauresia Sauresia cayemitae ANSP 38691 Haiti
#> 6 Sauresia Sauresia cayemitae ANSP 38673 Haiti
#> 7 Sauresia Sauresia cayemitae ANSP 38674 Haiti
#> 8 Sauresia Sauresia cayemitae ANSP 38675 Haiti
#> 9 Paratype Sauresia Sauresia cayemitae SBH 274212 Haiti
#> 10 Sauresia Sauresia cayemitae ANSP 38676 Haiti
#> 11 Holotype Sauresia Sauresia gracilis UNSM 328852 Haiti
#> 12 Paratype Sauresia Sauresia habichi ANSP 38681 Haiti
#> 13 Holotype Sauresia Sauresia habichi ANSP 38683 Haiti
#> 14 Holotype Sauresia Sauresia manicula ANSP 38667 Haiti
#> 15 Paratype Sauresia Sauresia manicula ANSP 38668 Haiti
#> 16 Paratype Sauresia Sauresia pangnolae ANSP 38690 Haiti
#> 17 Paratype Sauresia Sauresia pangnolae ANSP 38663 Haiti
#> 18 Paratype Sauresia Sauresia pangnolae ANSP 38664 Haiti
#> 19 Holotype Sauresia Sauresia pangnolae ANSP 38684 Haiti
#> 20 Sauresia Sauresia sepsoides UNSM 328846 Dominican Republic
#> 21 Sauresia Sauresia sepsoides UNSM 328850 Dominican Republic
#> 22 Sauresia Sauresia sepsoides UNSM 328851 Dominican Republic
#> 23 Paratype Sauresia Sauresia sepsoides ANSP 38678 Dominican Republic
#> 24 Paratype Sauresia Sauresia sepsoides ANSP 38670 Dominican Republic
#> 25 Paratype Sauresia Sauresia sepsoides ANSP 38671 Dominican Republic
#> 26 Paratype Sauresia Sauresia sepsoides ANSP 38672 Dominican Republic
#> 27 Paratype Sauresia Sauresia sepsoides ANSP 38666 Dominican Republic
#> 28 Paratype Sauresia Sauresia sepsoides ANSP 38680 Dominican Republic
#> 29 Sauresia Sauresia sepsoides SBH 193149 Dominican Republic
#> 30 Paratype Sauresia Sauresia sepsoides ANSP 38706 Dominican Republic
#> 31 Paratype Sauresia Sauresia sepsoides ANSP 38707 Dominican Republic
#> 32 Paratype Sauresia Sauresia sepsoides ANSP 38708 Dominican Republic
#> 33 Paratype Sauresia Sauresia sepsoides ANSP 38709 Dominican Republic
#> 34 Sauresia Sauresia sepsoides SBH 266746 Dominican Republic
#> 35 Sauresia Sauresia sepsoides SBH 266748 Dominican Republic
#> 36 Sauresia Sauresia sepsoides SBH 266749 Dominican Republic
#> 37 Sauresia Sauresia sepsoides SBH 266750 Dominican Republic
#> 38 Sauresia Sauresia sepsoides SBH 266754 Dominican Republic
#> 39 Sauresia Sauresia sepsoides SBH 267754 Dominican Republic
#> 40 Sauresia Sauresia sepsoides SBH 267755 Dominican Republic
#> 41 Sauresia Sauresia sepsoides SBH 267756 Dominican Republic
#> 42 Sauresia Sauresia sepsoides SBH 267757 Dominican Republic
#> 43 Sauresia Sauresia sepsoides SBH 267758 Dominican Republic
#> 44 Sauresia Sauresia sepsoides SBH 267773 Dominican Republic
#> 45 Sauresia Sauresia sepsoides SBH 267780 Dominican Republic
#> 46 Sauresia Sauresia sepsoides SBH 267781 Dominican Republic
#> 47 Paratype Sauresia Sauresia synoria SBH 160343 Dominican Republic
#> 48 Wetmorena Wetmorena surda SBH 266705 Dominican Republic
#> Province
#> 1 Sud-Est
#> 2
#> 3
#> 4
#> 5 Dept. de la Grand'Anse
#> 6 Grand'Anse
#> 7 Grand'Anse
#> 8 Grand'Anse
#> 9 Grand'Anse
#> 10 Grand'Anse
#> 11 Dept. du Sud
#> 12 Dept. de la Grand'Anse
#> 13 Dept. de la Grand'Anse
#> 14 L'Ouest
#> 15 L'Ouest
#> 16 Dept. de la Grand'Anse
#> 17 Dept. de la Grand'Anse
#> 18 Dept. de la Grand'Anse
#> 19 Nippes
#> 20 Hato Mayor
#> 21 Hato Mayor
#> 22 Hato Mayor
#> 23 La Altagracia
#> 24 Sanchez Ramirez Prov.
#> 25 Sanchez Ramirez Prov.
#> 26 Sanchez Ramirez Prov.
#> 27 Duarte Prov.
#> 28 Monte Plata Prov.
#> 29 Duarte Prov.
#> 30 Los Tabucos
#> 31 Los Tabucos
#> 32 Los Tabucos
#> 33 Los Tabucos
#> 34 Monte Plata
#> 35 Monte Plata
#> 36 Monte Plata
#> 37 Monte Plata
#> 38 Monte Plata
#> 39 Monte Plata
#> 40 Monte Plata
#> 41 Monte Plata
#> 42 Monte Plata
#> 43 Monte Plata
#> 44 Hato Mayor
#> 45 Parque Nacional Los Haitises
#> 46 Parque Nacional Los Haitises
#> 47 Pedernales
#> 48 Pedernales
#> Locality Elevation
#> 1 Morne D'Enfer 1433
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 Pestel 5.0 km S of 300
#> 6 Grande Cayemite (helipad-camp) 74
#> 7 Grande Cayemite (waypoint 166) 38
#> 8 Grande Cayemite (waypoint 166) 38
#> 9 Grande Cayemite (waypoint 166) 38
#> 10 Grande Cayemite (waypoint 166) 38
#> 11 Port Salut 10.3 km NW 10
#> 12 Marche Leon 8.0 km S of 435
#> 13 Marche Leon 8.0 km S of 435
#> 14 Berry 1630
#> 15 Berry 1630
#> 16 Pestel 11.8 km S of 550
#> 17 Baraderes 8.0 km SSW of 420
#> 18 Baraderes 8.0 km SSW of 420
#> 19 Morne Bois Pangnol 1170
#> 20 Sabana De La Mar 9.5 km W (airline) in Los Haitises NA
#> 21 El Valle ca 15 km W (on road to Trepada Alta) NA
#> 22 El Valle ca 15 km W (on road to Trepada Alta) NA
#> 23 La Zanga 7.5 km W of (at Rio Maimon) 25
#> 24 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 25 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 26 Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate) 35
#> 27 Batez Piedra on west side of Rio Pazabo 35
#> 28 Majagual 4.3 km N of 90
#> 29 Southern slopes of Loma Quita Espuela 775
#> 30 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 31 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 32 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 33 Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.) 455
#> 34 Los Limones footpath N of town 197
#> 35 Los Limones 3km S 275
#> 36 Los Limones 3km S 275
#> 37 Los Limones 3km S 275
#> 38 6km S Los Limones 305
#> 39 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 40 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 41 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 42 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 43 ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W 250
#> 44 14.1 km W El Valle; Lat: 19d0.393' N Long: 69d29.333' W 193
#> 45 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W 150
#> 46 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W 150
#> 47 Pedernales 22 km N at Rio Mulito 274
#> 48 N Los Arroyos 1660
#> Date Collected
#> 1
#> 2
#> 3
#> 4
#> 5 5/25/1991
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 10/28/1984
#> 12 5/28/1991
#> 13 5/28/1991
#> 14
#> 15
#> 16 5/25/1991
#> 17 6/7/1991
#> 18 6/7/1991
#> 19
#> 20 8/11/1984
#> 21 8/10/1984
#> 22 8/10/1984
#> 23 7/20/1991
#> 24 7/11/1993
#> 25 7/11/1993
#> 26 7/11/1993
#> 27 7/13/1993
#> 28 7/13/1993
#> 29 7/16/1993
#> 30 7/21/1993
#> 31 7/21/1993
#> 32 7/21/1993
#> 33 7/21/1993
#> 34 3/27/2004
#> 35 3/26/2004
#> 36 3/26/2004
#> 37 3/26/2004
#> 38 3/26/2004
#> 39 7/7/2006
#> 40 7/7/2006
#> 41 7/7/2006
#> 42 7/7/2006
#> 43 7/7/2006
#> 44
#> 45
#> 46
#> 47 6/22/1985
#> 48 3/23/2004
#> Collectors
#> 1
#> 2
#> 3
#> 4
#> 5 Richard Thomas and Manuel Leal
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 S. Blair Hedges and Richard Thomas
#> 12 S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer
#> 13 S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer
#> 14
#> 15
#> 16 Richard Thomas and Manuel Leal
#> 17 S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals
#> 18 S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals
#> 19
#> 20 S. Blair Hedges and Richard Thomas
#> 21 S. Blair Hedges and Richard Thomas
#> 22 S. Blair Hedges and Richard Thomas
#> 23 S. Blair Hedges Richard Thomas and Nicholas Plummer
#> 24 Manuel Leal Richard Thomas
#> 25 Manuel Leal Richard Thomas
#> 26 Manuel Leal Richard Thomas
#> 27 Richard Thomas Manuel Leal and Herman Dominicia
#> 28 Richard Thomas
#> 29 Herman Dominicia Richard Thomas
#> 30 Richard Thomas
#> 31 Richard Thomas
#> 32 Richard Thomas
#> 33 Richard Thomas
#> 34 Richard Thomas
#> 35 Richard Thomas
#> 36 Richard Thomas
#> 37 Richard Thomas
#> 38 Richard Thomas
#> 39 RT
#> 40 RT
#> 41 RT
#> 42 RT
#> 43 RT
#> 44 RT EF and SBH
#> 45
#> 46
#> 47 Richard Thomas and S. Blair Hedges
#> 48
#> Remarks
#> 1
#> 2
#> 3
#> 4
#> 5 under rocks and logs
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11 day; under objects and in leaf litter
#> 12
#> 13
#> 14
#> 15
#> 16
#> 17 eleuths found on limestone rocks A. cybotes and A. manticola found sleeping on ferns E. abbotti female found in leaf litter
#> 18 eleuths found on limestone rocks A. cybotes and A. manticola found sleeping on ferns E. abbotti female found in leaf litter
#> 19
#> 20 day; all under rocks along a dry slope ca. 1 mile SE of base camp (C-159) by trail (not straight)
#> 21 under rocks and logs in pasture limestone outcrops nearby; day
#> 22 under rocks and logs in pasture limestone outcrops nearby; day
#> 23
#> 24 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 25 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 26 rocky open hillside in cut-over kerst hills; many limestone rocks
#> 27 locality = ca. 10.5 km airline NNE of Cervicos
#> 28 coffee grove in the Haitises; some rocks but not a lot and some rotten logs
#> 29
#> 30 cacao-coffee grove
#> 31 cacao-coffee grove
#> 32 cacao-coffee grove
#> 33 cacao-coffee grove
#> 34
#> 35
#> 36
#> 37
#> 38
#> 39
#> 40
#> 41
#> 42
#> 43
#> 44
#> 45
#> 46
#> 47 night; E inoptatus resting on leaf 6" high on stream bank; Epicrates striatus moving in a tree 5' above the stream; Sauresia under rock
#> 48
#> Latitude Longitude SVL Pattern Head Markings Nuchal Lines
#> 1 18.33005 -72.37095 69.10 0 0 0
#> 2 NA NA 53.80 1 1 0
#> 3 NA NA 49.40 0 0 0
#> 4 NA NA 64.80 1 0 0
#> 5 18.51329 -73.78463 58.10 5 1 1
#> 6 18.63316 -73.75524 56.80 2 1 1
#> 7 18.63562 -73.75175 47.80 4 1 1
#> 8 18.63562 -73.75175 53.20 4 1 1
#> 9 18.63562 -73.75175 49.37 5 1 1
#> 10 18.63562 -73.75175 53.80 4 1 1
#> 11 18.14086 -73.96780 51.14 NA 1 1
#> 12 18.51678 -74.08311 59.70 3 1 1
#> 13 18.51678 -74.08311 50.50 5 1 1
#> 14 18.30795 -72.25389 69.00 3 NA 1
#> 15 18.30795 -72.25389 59.60 3 NA 1
#> 16 18.47942 -73.78744 54.30 2 0 0
#> 17 18.44032 -73.66756 66.70 1 0 1
#> 18 18.44032 -73.66756 54.30 1 0 1
#> 19 18.41869 -73.77512 66.10 1 0 0
#> 20 19.05293 -69.47899 NA NA NA NA
#> 21 NA NA NA NA NA NA
#> 22 NA NA NA NA NA NA
#> 23 NA NA 62.80 2 0 0
#> 24 19.10370 -70.05310 62.80 2 0 0
#> 25 19.10370 -70.05310 59.10 1 0 0
#> 26 19.10370 -70.05310 54.80 2 1 0
#> 27 19.06997 -69.90815 48.60 1 0 0
#> 28 19.07539 -69.82842 54.60 2 1 0
#> 29 NA NA 32.75 2 1 1
#> 30 NA NA 65.20 2 0 1
#> 31 NA NA 59.60 1 0 0
#> 32 NA NA 58.90 1 0 0
#> 33 NA NA 59.00 2 1 1
#> 34 NA NA NA NA NA NA
#> 35 NA NA NA NA NA NA
#> 36 NA NA NA NA NA NA
#> 37 NA NA NA NA NA NA
#> 38 NA NA NA NA NA NA
#> 39 19.01932 -69.73766 NA NA NA NA
#> 40 19.01932 -69.73766 NA NA NA NA
#> 41 19.01932 -69.73766 NA NA NA NA
#> 42 19.01932 -69.73766 NA NA NA NA
#> 43 19.01932 -69.73766 NA NA NA NA
#> 44 NA NA NA NA NA NA
#> 45 19.06667 -69.57127 NA NA NA NA
#> 46 19.06667 -69.57127 NA NA NA NA
#> 47 18.15440 -71.75810 63.66 0 1 1
#> 48 18.25790 -71.74460 NA NA NA NA
#> Dots in Lateral Band Mental to Vent Scale Count Midbody ScaleCount
#> 1 0 123 38
#> 2 0 121 39
#> 3 0 124 37
#> 4 0 127 37
#> 5 0 117 37
#> 6 0 117 36
#> 7 0 111 32
#> 8 0 115 33
#> 9 0 NA 34
#> 10 0 110 36
#> 11 0 103 36
#> 12 0 122 41
#> 13 0 125 38
#> 14 0 129 37
#> 15 0 123 37
#> 16 1 109 38
#> 17 1 113 39
#> 18 1 104 39
#> 19 1 115 42
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 0 118 36
#> 24 0 114 35
#> 25 0 117 37
#> 26 0 111 37
#> 27 0 116 36
#> 28 0 108 36
#> 29 0 116 36
#> 30 0 119 37
#> 31 0 118 36
#> 32 0 115 36
#> 33 0 114 36
#> 34 NA NA NA
#> 35 NA NA NA
#> 36 NA NA NA
#> 37 NA NA NA
#> 38 NA NA NA
#> 39 NA NA NA
#> 40 NA NA NA
#> 41 NA NA NA
#> 42 NA NA NA
#> 43 NA NA NA
#> 44 NA NA NA
#> 45 NA NA NA
#> 46 NA NA NA
#> 47 0 123 34
#> 48 NA NA NA
#> Total Finger Lamella Strigae on Ten Scales Total Toe Length
#> 1 17 103 7.80
#> 2 17 103 8.04
#> 3 17 NA NA
#> 4 17 138 7.94
#> 5 19 84 7.80
#> 6 18 104 7.06
#> 7 19 94 6.71
#> 8 18 93 7.13
#> 9 16 89 5.69
#> 10 18 92 7.41
#> 11 18 100 7.07
#> 12 18 113 7.72
#> 13 19 89 6.63
#> 14 17 150 8.32
#> 15 17 119 6.68
#> 16 15 96 7.42
#> 17 19 109 8.82
#> 18 18 104 7.77
#> 19 17 92 7.67
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 17 101 7.70
#> 24 16 114 6.79
#> 25 16 96 6.35
#> 26 17 97 6.41
#> 27 16 NA NA
#> 28 17 104 8.24
#> 29 14 NA NA
#> 30 15 105 7.89
#> 31 17 97 7.14
#> 32 17 94 7.09
#> 33 17 106 7.86
#> 34 NA NA NA
#> 35 NA NA NA
#> 36 NA NA NA
#> 37 NA NA NA
#> 38 NA NA NA
#> 39 NA NA NA
#> 40 NA NA NA
#> 41 NA NA NA
#> 42 NA NA NA
#> 43 NA NA NA
#> 44 NA NA NA
#> 45 NA NA NA
#> 46 NA NA NA
#> 47 18 111 6.68
#> 48 NA NA NA
#> Scale Under Eye to Lip Distance Eye Length Arm Length Ear Width
#> 1 0.15 1.69 7.06 0.49
#> 2 0.14 1.70 7.31 0.31
#> 3 NA NA NA NA
#> 4 0.17 1.49 7.14 0.43
#> 5 0.09 1.49 7.29 0.41
#> 6 0.13 1.57 6.58 0.46
#> 7 0.06 1.27 5.49 0.50
#> 8 0.13 1.46 5.66 0.58
#> 9 0.14 1.29 5.57 0.55
#> 10 0.03 1.55 6.34 0.63
#> 11 0.13 1.52 5.54 0.34
#> 12 0.12 1.38 7.04 0.38
#> 13 0.03 1.21 6.61 0.34
#> 14 0.13 1.58 7.93 0.60
#> 15 0.10 1.38 7.09 0.36
#> 16 0.08 1.64 6.84 0.44
#> 17 0.10 1.93 7.95 0.61
#> 18 0.07 1.51 6.78 0.60
#> 19 0.12 1.69 7.54 0.45
#> 20 NA NA NA NA
#> 21 NA NA NA NA
#> 22 NA NA NA NA
#> 23 0.12 1.55 6.86 0.59
#> 24 0.19 1.57 5.95 0.50
#> 25 0.16 1.47 5.81 0.36
#> 26 0.15 1.49 6.20 0.37
#> 27 NA NA NA NA
#> 28 0.11 1.36 6.81 0.54
#> 29 NA NA NA NA
#> 30 0.14 1.62 6.41 0.40
#> 31 0.13 1.51 6.53 0.49
#> 32 0.16 1.47 6.27 0.30
#> 33 0.12 1.46 7.01 0.32
#> 34 NA NA NA NA
#> 35 NA NA NA NA
#> 36 NA NA NA NA
#> 37 NA NA NA NA
#> 38 NA NA NA NA
#> 39 NA NA NA NA
#> 40 NA NA NA NA
#> 41 NA NA NA NA
#> 42 NA NA NA NA
#> 43 NA NA NA NA
#> 44 NA NA NA NA
#> 45 NA NA NA NA
#> 46 NA NA NA NA
#> 47 0.20 1.57 5.82 0.39
#> 48 NA NA NA NA
#> Rostral Width Rostral Height Head Length Mental Width Post Mental Width
#> 1 1.55 0.76 9.42 1.11 1.62
#> 2 1.50 0.78 8.20 1.10 1.45
#> 3 NA NA NA NA NA
#> 4 1.57 0.74 8.91 1.04 1.49
#> 5 1.41 0.75 8.02 0.85 1.42
#> 6 1.38 0.80 8.87 0.91 1.29
#> 7 1.16 0.53 7.02 0.83 1.15
#> 8 1.19 0.72 7.20 0.77 1.24
#> 9 1.39 0.51 6.61 0.82 1.23
#> 10 1.31 0.73 8.13 0.96 1.35
#> 11 1.33 0.70 8.03 0.90 1.41
#> 12 1.46 0.80 8.94 0.93 1.39
#> 13 1.43 0.59 7.16 0.92 1.18
#> 14 1.73 0.91 9.83 1.15 1.49
#> 15 1.36 0.72 7.78 0.88 1.27
#> 16 1.38 0.80 8.34 0.79 1.11
#> 17 1.94 0.94 10.10 1.27 1.65
#> 18 1.39 0.76 8.30 0.95 1.31
#> 19 1.47 0.81 8.62 0.81 1.57
#> 20 NA NA NA NA NA
#> 21 NA NA NA NA NA
#> 22 NA NA NA NA NA
#> 23 1.72 0.90 9.28 1.09 1.42
#> 24 2.00 1.00 8.21 0.86 1.22
#> 25 1.50 0.81 7.87 0.97 1.29
#> 26 1.46 0.95 8.04 0.89 1.12
#> 27 NA NA 7.34 NA NA
#> 28 1.45 0.75 8.13 0.78 1.18
#> 29 NA NA NA NA NA
#> 30 2.00 1.00 8.88 0.94 1.43
#> 31 1.53 0.74 8.44 0.91 1.25
#> 32 1.60 0.81 8.42 1.11 1.33
#> 33 1.60 0.66 9.11 0.87 1.27
#> 34 NA NA NA NA NA
#> 35 NA NA NA NA NA
#> 36 NA NA NA NA NA
#> 37 NA NA NA NA NA
#> 38 NA NA NA NA NA
#> 39 NA NA NA NA NA
#> 40 NA NA NA NA NA
#> 41 NA NA NA NA NA
#> 42 NA NA NA NA NA
#> 43 NA NA NA NA NA
#> 44 NA NA NA NA NA
#> 45 NA NA NA NA NA
#> 46 NA NA NA NA NA
#> 47 1.53 0.84 7.80 0.77 1.54
#> 48 NA NA NA NA NA
#> Cloaca Width Prefrontal Width Largest Supraoccular Width Finger III Length
#> 1 4.21 2.09 1.29 1.46
#> 2 3.67 2.14 1.33 1.54
#> 3 NA NA NA NA
#> 4 3.96 2.16 1.23 1.49
#> 5 3.54 1.98 0.97 1.54
#> 6 3.53 2.01 1.20 1.40
#> 7 2.67 1.74 1.04 1.25
#> 8 3.32 1.71 1.05 1.32
#> 9 3.03 1.66 1.11 1.13
#> 10 3.31 1.88 1.07 1.28
#> 11 3.67 1.95 1.25 1.00
#> 12 3.99 2.25 1.33 1.40
#> 13 3.07 2.00 1.05 1.37
#> 14 4.42 2.50 1.39 1.52
#> 15 3.16 1.98 1.11 1.32
#> 16 3.70 2.01 1.15 1.38
#> 17 4.05 2.47 1.49 1.53
#> 18 3.66 2.08 1.43 1.38
#> 19 4.20 NA 1.17 1.53
#> 20 NA NA NA NA
#> 21 NA NA NA NA
#> 22 NA NA NA NA
#> 23 3.87 2.36 1.31 1.33
#> 24 3.63 2.11 1.41 1.17
#> 25 3.78 2.09 1.12 1.03
#> 26 3.01 2.03 1.01 1.20
#> 27 NA NA NA NA
#> 28 3.37 2.05 1.06 1.23
#> 29 NA NA NA NA
#> 30 4.06 2.28 1.05 1.20
#> 31 3.48 1.98 1.11 1.28
#> 32 3.23 2.12 1.00 1.35
#> 33 3.63 2.31 1.28 1.38
#> 34 NA NA NA NA
#> 35 NA NA NA NA
#> 36 NA NA NA NA
#> 37 NA NA NA NA
#> 38 NA NA NA NA
#> 39 NA NA NA NA
#> 40 NA NA NA NA
#> 41 NA NA NA NA
#> 42 NA NA NA NA
#> 43 NA NA NA NA
#> 44 NA NA NA NA
#> 45 NA NA NA NA
#> 46 NA NA NA NA
#> 47 3.58 2.04 1.06 1.46
#> 48 NA NA NA NA
#> Ear to Eye Distance Head Width Frontal Width Frontal Length
#> 1 4.79 6.77 NA NA
#> 2 4.23 6.12 2.31 2.82
#> 3 NA NA NA NA
#> 4 4.49 6.21 2.55 3.18
#> 5 3.87 5.91 2.06 2.82
#> 6 3.73 6.08 1.91 2.51
#> 7 3.29 5.21 1.79 2.36
#> 8 3.26 5.55 1.87 2.33
#> 9 2.97 5.02 1.63 2.23
#> 10 3.64 5.73 2.02 2.43
#> 11 3.90 5.43 2.03 2.45
#> 12 4.36 6.95 2.14 2.98
#> 13 3.41 5.63 1.88 2.54
#> 14 5.17 8.14 2.55 3.13
#> 15 4.03 5.67 NA 2.59
#> 16 4.04 6.24 2.12 2.60
#> 17 4.97 7.15 2.74 3.60
#> 18 4.05 6.49 2.11 2.76
#> 19 4.59 6.74 2.06 2.96
#> 20 NA NA NA NA
#> 21 NA NA NA NA
#> 22 NA NA NA NA
#> 23 4.77 6.79 2.30 2.83
#> 24 3.85 5.88 2.35 2.79
#> 25 3.78 5.57 2.20 2.65
#> 26 3.75 5.20 2.12 2.57
#> 27 NA NA NA NA
#> 28 3.77 5.59 2.06 2.72
#> 29 NA NA NA NA
#> 30 4.20 6.43 2.25 2.92
#> 31 4.32 6.04 2.04 2.76
#> 32 4.03 5.89 2.08 2.87
#> 33 4.74 6.44 2.26 3.27
#> 34 NA NA NA NA
#> 35 NA NA NA NA
#> 36 NA NA NA NA
#> 37 NA NA NA NA
#> 38 NA NA NA NA
#> 39 NA NA NA NA
#> 40 NA NA NA NA
#> 41 NA NA NA NA
#> 42 NA NA NA NA
#> 43 NA NA NA NA
#> 44 NA NA NA NA
#> 45 NA NA NA NA
#> 46 NA NA NA NA
#> 47 3.76 5.93 NA 2.37
#> 48 NA NA NA NA
#> SVL_standardized_SVL Pattern_standardized_SVL Head Markings_standardized_SVL
#> 1 1 0.00000000 0.00000000
#> 2 1 0.01858736 0.01858736
#> 3 1 0.00000000 0.00000000
#> 4 1 0.01543210 0.00000000
#> 5 1 0.08605852 0.01721170
#> 6 1 0.03521127 0.01760563
#> 7 1 0.08368201 0.02092050
#> 8 1 0.07518797 0.01879699
#> 9 1 0.10127608 0.02025522
#> 10 1 0.07434944 0.01858736
#> 11 1 NA 0.01955417
#> 12 1 0.05025126 0.01675042
#> 13 1 0.09900990 0.01980198
#> 14 1 0.04347826 NA
#> 15 1 0.05033557 NA
#> 16 1 0.03683241 0.00000000
#> 17 1 0.01499250 0.00000000
#> 18 1 0.01841621 0.00000000
#> 19 1 0.01512859 0.00000000
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 1 0.03184713 0.00000000
#> 24 1 0.03184713 0.00000000
#> 25 1 0.01692047 0.00000000
#> 26 1 0.03649635 0.01824818
#> 27 1 0.02057613 0.00000000
#> 28 1 0.03663004 0.01831502
#> 29 1 0.06106870 0.03053435
#> 30 1 0.03067485 0.00000000
#> 31 1 0.01677852 0.00000000
#> 32 1 0.01697793 0.00000000
#> 33 1 0.03389831 0.01694915
#> 34 NA NA NA
#> 35 NA NA NA
#> 36 NA NA NA
#> 37 NA NA NA
#> 38 NA NA NA
#> 39 NA NA NA
#> 40 NA NA NA
#> 41 NA NA NA
#> 42 NA NA NA
#> 43 NA NA NA
#> 44 NA NA NA
#> 45 NA NA NA
#> 46 NA NA NA
#> 47 1 0.00000000 0.01570845
#> 48 NA NA NA
#> Head Width_standardized_SVL Frontal Width_standardized_SVL
#> 1 0.09797395 NA
#> 2 0.11375465 0.04293680
#> 3 NA NA
#> 4 0.09583333 0.03935185
#> 5 0.10172117 0.03545611
#> 6 0.10704225 0.03362676
#> 7 0.10899582 0.03744770
#> 8 0.10432331 0.03515038
#> 9 0.10168118 0.03301600
#> 10 0.10650558 0.03754647
#> 11 0.10617912 0.03969496
#> 12 0.11641541 0.03584590
#> 13 0.11148515 0.03722772
#> 14 0.11797101 0.03695652
#> 15 0.09513423 NA
#> 16 0.11491713 0.03904236
#> 17 0.10719640 0.04107946
#> 18 0.11952118 0.03885820
#> 19 0.10196672 0.03116490
#> 20 NA NA
#> 21 NA NA
#> 22 NA NA
#> 23 0.10812102 0.03662420
#> 24 0.09363057 0.03742038
#> 25 0.09424704 0.03722504
#> 26 0.09489051 0.03868613
#> 27 NA NA
#> 28 0.10238095 0.03772894
#> 29 NA NA
#> 30 0.09861963 0.03450920
#> 31 0.10134228 0.03422819
#> 32 0.10000000 0.03531409
#> 33 0.10915254 0.03830508
#> 34 NA NA
#> 35 NA NA
#> 36 NA NA
#> 37 NA NA
#> 38 NA NA
#> 39 NA NA
#> 40 NA NA
#> 41 NA NA
#> 42 NA NA
#> 43 NA NA
#> 44 NA NA
#> 45 NA NA
#> 46 NA NA
#> 47 0.09315112 NA
#> 48 NA NAprocess_phylo_count(): Count the number of individuals
per group in a phylogeny
process_specimen_count(): Count the number of
individualsper group in a character dataset
process_specimen_count(
sauresia_morpho3,
grouped_by = "Species")
#> # A tibble: 10 × 2
#> Group Specimen_Count
#> <chr> <int>
#> 1 Sauresia agramma 4
#> 2 Sauresia cayemitae 6
#> 3 Sauresia gracilis 1
#> 4 Sauresia habichi 2
#> 5 Sauresia manicula 2
#> 6 Sauresia pangnolae 4
#> 7 Sauresia sepsoides 27
#> 8 Sauresia synoria 1
#> 9 Wetmorena surda 1
#> 10 Total 48process_phylo_names(): Update individual names in the
phylogenies to be more legible and match those in other datasets
process_data_matches(): Check for consistency in
individual names between datasets
process_data_matches(
phy1 = sauresia_ML_rooted,
data1 = sauresia_morpho3,
data1_column = "Name in Tree")
#> Specimens that do not match from phylogeny:
#> 191850_Sauresia_cayemitae_HT_Pestel, 266705_Wetmorena_surda_DO_N_Los_Arroyos
#>
#> Specimens that do not match from dataset:
#> 191850_Sauresia_sepsoides_HT_Pestel, 266705_Wetmorena_haetiana_surda_DO_N_Los_Arroyos4. Character (Morphological) Functions
trait_filter(): Check which individuals fall
above/below a threshold for a given trait
trait_min_max(): Check which group has the min and max
value for a given trait
trait_summary(): Compute the summary statistics for a
given trait per group
trait_summary(
data = sauresia_morpho3,
grouped_by = "Species",
trait_column = "SVL")
#> # A tibble: 9 × 4
#> Species Mean Median SD
#> <chr> <dbl> <dbl> <dbl>
#> 1 Sauresia agramma 59.3 59.3 9.21
#> 2 Sauresia cayemitae 53.2 53.5 4.03
#> 3 Sauresia gracilis 51.1 51.1 NA
#> 4 Sauresia habichi 55.1 55.1 6.51
#> 5 Sauresia manicula 64.3 64.3 6.65
#> 6 Sauresia pangnolae 60.4 60.2 6.99
#> 7 Sauresia sepsoides 56.2 59 9.03
#> 8 Sauresia synoria 63.7 63.7 NA
#> 9 Wetmorena surda NaN NA NAtrait_compare(): Compare the distribution of a trait
between two groups (scatterplots and interactive box plots)
trait_compare(
data = sauresia_morpho3,
group_by_column = "Species",
group_values = c("Sauresia cayemitae", "Sauresia pangnolae"),
traits = c("SVL", "Total Toe Length"))
#> $box_plots
#> $box_plots[[1]]
#>
#> $box_plots[[2]]trait_not_separated(): Check which groups cannot be
distinguished pairwise based on the included traits
trait_not_separated(
data = sauresia_morpho3,
trait_columns = c("SVL", "Pattern", "Head Markings",
"Head Width", "Frontal Width"),
grouped_by = "Species")
#> The following pairs could not be separated by any trait:
#> Sauresia agramma vs Sauresia pangnolae
#> Sauresia agramma vs Sauresia sepsoides
#> Sauresia agramma vs Wetmorena surda
#> Sauresia cayemitae vs Sauresia gracilis
#> Sauresia cayemitae vs Sauresia habichi
#> Sauresia cayemitae vs Sauresia sepsoides
#> Sauresia cayemitae vs Wetmorena surda
#> Sauresia gracilis vs Wetmorena surda
#> Sauresia habichi vs Wetmorena surda
#> Sauresia manicula vs Wetmorena surda
#> Sauresia pangnolae vs Sauresia sepsoides
#> Sauresia pangnolae vs Wetmorena surda
#> Sauresia sepsoides vs Wetmorena surda
#> Sauresia synoria vs Wetmorena surda5. Geographic Functions
geo_range(): Print the max and min longitude and
latitude coordinated for each group
geo_range(
sauresia_morpho3,
grouped_by = "Species",
lat_col = "Latitude",
long_col = "Longitude")
#> # A tibble: 9 × 6
#> Species Count Min_Lat Max_Lat Min_Long Max_Long
#> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 Sauresia agramma 1 18.330052 18.330052 -72.37095 -72.37095
#> 2 Sauresia cayemitae 6 18.513286 18.635615 -73.784632 -73.751749
#> 3 Sauresia gracilis 1 18.140859 18.140859 -73.967801 -73.967801
#> 4 Sauresia habichi 2 18.516777 18.516777 -74.083109 -74.083109
#> 5 Sauresia manicula 2 18.307945 18.307945 -72.253894 -72.253894
#> 6 Sauresia pangnolae 4 18.418689 18.479421 -73.78744 -73.667556
#> 7 Sauresia sepsoides 13 19.01932 19.1037 -70.0531 -69.47899
#> 8 Sauresia synoria 1 18.1544 18.1544 -71.7581 -71.7581
#> 9 Wetmorena surda 1 18.2579 18.2579 -71.7446 -71.7446geo_convex_hull(): Calculate the area of the convex
hull for each group with more than three sets of coordinates
geo_convex_hull(
sauresia_morpho3,
grouped_by = "Species",
lat_col = "Latitude",
long_col = "Longitude",
area_unit = "km^2")
#> Group Convex_Hull_Area geometry
#> 1 Sauresia cayemitae 2.029136 POLYGON ((-73.78463 18.5132...
#> 2 Sauresia pangnolae 39.877357 POLYGON ((-73.78744 18.4794...
#> 3 Sauresia sepsoides 208.519353 POLYGON ((-70.0531 19.1037,...geo_plot_map(): Plot an interactive map showing
occurance data and convex hulls for groups where applicable
geo_range_overlaps(): Print a table showing which
groups have overlapping ranges (
Calculated using convex hulls (3+ sets of coordinates), lines (2 sets of coordinates), and points (1 set of coordinates)
geo_range_overlaps(
sauresia_morpho3,
group_by = "Species",
lat_col = "Latitude",
long_col = "Longitude")
#> Warning: package 'sf' was built under R version 4.3.3
#> Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
#> Sauresia agramma Sauresia cayemitae Sauresia gracilis
#> Sauresia agramma "N/A" "FALSE" "FALSE"
#> Sauresia cayemitae "FALSE" "N/A" "FALSE"
#> Sauresia gracilis "FALSE" "FALSE" "N/A"
#> Sauresia habichi "FALSE" "FALSE" "FALSE"
#> Sauresia manicula "FALSE" "FALSE" "FALSE"
#> Sauresia pangnolae "FALSE" "FALSE" "FALSE"
#> Sauresia sepsoides "FALSE" "FALSE" "FALSE"
#> Sauresia synoria "FALSE" "FALSE" "FALSE"
#> Wetmorena surda "FALSE" "FALSE" "FALSE"
#> Sauresia habichi Sauresia manicula Sauresia pangnolae
#> Sauresia agramma "FALSE" "FALSE" "FALSE"
#> Sauresia cayemitae "FALSE" "FALSE" "FALSE"
#> Sauresia gracilis "FALSE" "FALSE" "FALSE"
#> Sauresia habichi "N/A" "FALSE" "FALSE"
#> Sauresia manicula "FALSE" "N/A" "FALSE"
#> Sauresia pangnolae "FALSE" "FALSE" "N/A"
#> Sauresia sepsoides "FALSE" "FALSE" "FALSE"
#> Sauresia synoria "FALSE" "FALSE" "FALSE"
#> Wetmorena surda "FALSE" "FALSE" "FALSE"
#> Sauresia sepsoides Sauresia synoria Wetmorena surda
#> Sauresia agramma "FALSE" "FALSE" "FALSE"
#> Sauresia cayemitae "FALSE" "FALSE" "FALSE"
#> Sauresia gracilis "FALSE" "FALSE" "FALSE"
#> Sauresia habichi "FALSE" "FALSE" "FALSE"
#> Sauresia manicula "FALSE" "FALSE" "FALSE"
#> Sauresia pangnolae "FALSE" "FALSE" "FALSE"
#> Sauresia sepsoides "N/A" "FALSE" "FALSE"
#> Sauresia synoria "FALSE" "N/A" "FALSE"
#> Wetmorena surda "FALSE" "FALSE" "N/A"6. Phylogenetic Functions
phylo_tree_summary(): Get summary stats for the support
or time values in a phylogeny
phylo_tree_summary(
tree = sauresia_ML_rooted_named,
method = "ML")
#> Warning in phylo_tree_summary(tree = sauresia_ML_rooted_named, method = "ML"):
#> NAs introduced by coercion
#> $num_nodes
#> [1] 47
#>
#> $max_depth
#> [1] 0.2227683
#>
#> $bootstrap_summary
#> $bootstrap_summary$min
#> [1] 11
#>
#> $bootstrap_summary$max
#> [1] 100
#>
#> $bootstrap_summary$mean
#> [1] 68.17778
#>
#> $bootstrap_summary$mode
#> [1] 99
#>
#> $bootstrap_summary$median
#> [1] 77
#>
#> $bootstrap_summary$sd
#> [1] 29.61748phylo_clade_support(): Get summary stats for the
support or time for a specific group in the phylogeny
phylo_clade_support(
sauresia_ML_rooted_named,
"sepsoides",
method = "ML")
#> Warning in phylo_node_table(tree, method): NAs introduced by coercion
#> Node
#> 1 49
#> 2 50
#> 3 51
#> 4 52
#> 5 53
#> 6 54
#> 7 55
#> 8 56
#> 9 57
#> 10 58
#> 11 59
#> 12 60
#> 13 61
#> 14 62
#> 15 63
#> 16 64
#> 17 65
#> 18 66
#> 19 67
#> 20 68
#> 21 69
#> 22 70
#> 23 71
#> 24 72
#> 25 73
#> 26 74
#> 27 75
#> 28 76
#> 29 77
#> 30 78
#> 31 79
#> 32 80
#> 33 81
#> 34 82
#> 35 83
#> 36 84
#> 37 85
#> 38 86
#> 39 87
#> 40 88
#> 41 89
#> 42 90
#> 43 91
#> 44 92
#> 45 93
#> 46 94
#> 47 95
#> Taxa
#> 1 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2, Wetmorena surda 1
#> 2 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 3 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1
#> 4 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 5 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 6 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 7 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 8 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25
#> 9 Sauresia sepsoides 3, Sauresia sepsoides 25
#> 10 Sauresia sepsoides 26, Sauresia sepsoides 27
#> 11 Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 12 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 13 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 14 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 15 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17
#> 16 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 17 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20
#> 18 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14
#> 19 Sauresia sepsoides 5, Sauresia sepsoides 7
#> 20 Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 21 Sauresia sepsoides 8, Sauresia sepsoides 16
#> 22 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 23 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 24 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 25 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 26 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 27 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 28 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 29 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 30 Sauresia sepsoides 13, Sauresia sepsoides 21
#> 31 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 32 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2
#> 33 Sauresia manicula 1, Sauresia manicula 2
#> 34 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 35 Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 36 Sauresia agramma 3, Sauresia agramma 4
#> 37 Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 38 Sauresia pangnolae 1, Sauresia pangnolae 4
#> 39 Sauresia pangnolae 2, Sauresia pangnolae 3
#> 40 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> 41 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 42 Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 43 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 44 Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 45 Sauresia cayemitae 4, Sauresia cayemitae 6
#> 46 Sauresia habichi 1, Sauresia habichi 2
#> 47 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> Support_or_Time
#> 1 NA
#> 2 57
#> 3 68
#> 4 99
#> 5 99
#> 6 100
#> 7 58
#> 8 20
#> 9 22
#> 10 36
#> 11 80
#> 12 99
#> 13 35
#> 14 14
#> 15 11
#> 16 16
#> 17 18
#> 18 86
#> 19 96
#> 20 70
#> 21 41
#> 22 23
#> 23 38
#> 24 37
#> 25 77
#> 26 36
#> 27 95
#> 28 72
#> 29 69
#> 30 79
#> 31 94
#> 32 99
#> 33 99
#> 34 99
#> 35 72
#> 36 65
#> 37 100
#> 38 90
#> 39 79
#> 40 93
#> 41 99
#> 42 78
#> 43 93
#> 44 74
#> 45 86
#> 46 97
#> 47 NA
#>
#> ### Node Support Summary for sepsoides ###
#>
#> The following node values were used for the calculations:
#> Node Support_or_Time
#> 5 53 99
#> 6 54 100
#> 7 55 58
#> 8 56 20
#> 9 57 22
#> 10 58 36
#> 11 59 80
#> 12 60 99
#> 13 61 35
#> 14 62 14
#> 15 63 11
#> 16 64 16
#> 17 65 18
#> 18 66 86
#> 19 67 96
#> 20 68 70
#> 21 69 41
#> 22 70 23
#> 23 71 38
#> 24 72 37
#> 25 73 77
#> 26 74 36
#> 27 75 95
#> 28 76 72
#> 29 77 69
#> 30 78 79
#> Taxa
#> 5 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 6 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 7 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 8 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25
#> 9 Sauresia sepsoides 3, Sauresia sepsoides 25
#> 10 Sauresia sepsoides 26, Sauresia sepsoides 27
#> 11 Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 12 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 13 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 14 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 15 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17
#> 16 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 17 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20
#> 18 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14
#> 19 Sauresia sepsoides 5, Sauresia sepsoides 7
#> 20 Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 21 Sauresia sepsoides 8, Sauresia sepsoides 16
#> 22 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 23 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 24 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 25 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 26 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 27 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 28 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 29 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 30 Sauresia sepsoides 13, Sauresia sepsoides 21
#> $mean
#> [1] 54.88462
#>
#> $median
#> [1] 49.5
#>
#> $sd
#> [1] 31.18888
#>
#> $min
#> [1] 11
#>
#> $max
#> [1] 100phylo_divergence_histogram(): Plot a histogram of
divergence dates from a timetree
#### phylo_taxa_divergence_hist(): Plot a histogram
comparing divergence times between multiple taxa in a timetree
phylo_taxa_divergence_hist(
tree = sauresia_T_named,
taxa_list = c("sepsoides", "agramma", "cayemitae"),
colors = c("darkseagreen", "deeppink", "pink"),
bin_width = 2)
#> Node
#> 1 48
#> 2 49
#> 3 50
#> 4 51
#> 5 52
#> 6 53
#> 7 54
#> 8 55
#> 9 56
#> 10 57
#> 11 58
#> 12 59
#> 13 60
#> 14 61
#> 15 62
#> 16 63
#> 17 64
#> 18 65
#> 19 66
#> 20 67
#> 21 68
#> 22 69
#> 23 70
#> 24 71
#> 25 72
#> 26 73
#> 27 74
#> 28 75
#> 29 76
#> 30 77
#> 31 78
#> 32 79
#> 33 80
#> 34 81
#> 35 82
#> 36 83
#> 37 84
#> 38 85
#> 39 86
#> 40 87
#> 41 88
#> 42 89
#> 43 90
#> 44 91
#> 45 92
#> 46 93
#> Taxa
#> 1 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> 2 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 3 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1
#> 4 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 5 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 6 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 7 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 8 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25
#> 9 Sauresia sepsoides 3, Sauresia sepsoides 25
#> 10 Sauresia sepsoides 26, Sauresia sepsoides 27
#> 11 Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 12 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 13 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 14 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 15 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17
#> 16 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 17 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20
#> 18 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14
#> 19 Sauresia sepsoides 5, Sauresia sepsoides 7
#> 20 Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 21 Sauresia sepsoides 8, Sauresia sepsoides 16
#> 22 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 23 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 24 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 25 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 26 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 27 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 28 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 29 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 30 Sauresia sepsoides 13, Sauresia sepsoides 21
#> 31 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 32 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2
#> 33 Sauresia manicula 1, Sauresia manicula 2
#> 34 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 35 Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 36 Sauresia agramma 3, Sauresia agramma 4
#> 37 Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 38 Sauresia pangnolae 1, Sauresia pangnolae 4
#> 39 Sauresia pangnolae 2, Sauresia pangnolae 3
#> 40 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> 41 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 42 Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 43 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 44 Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 45 Sauresia cayemitae 4, Sauresia cayemitae 6
#> 46 Sauresia habichi 1, Sauresia habichi 2
#> Support_or_Time
#> 1 4.98
#> 2 4.55
#> 3 4.37
#> 4 2.47
#> 5 1.07
#> 6 0.09
#> 7 0.04
#> 8 0.04
#> 9 0.04
#> 10 0.04
#> 11 1.07
#> 12 0.01
#> 13 0.01
#> 14 0.01
#> 15 0.00
#> 16 0.00
#> 17 0.00
#> 18 0.00
#> 19 0.00
#> 20 0.00
#> 21 0.00
#> 22 0.00
#> 23 0.00
#> 24 0.00
#> 25 0.00
#> 26 0.00
#> 27 0.00
#> 28 0.01
#> 29 0.01
#> 30 0.01
#> 31 2.02
#> 32 1.05
#> 33 0.00
#> 34 0.15
#> 35 0.00
#> 36 0.00
#> 37 0.70
#> 38 0.17
#> 39 0.36
#> 40 1.71
#> 41 0.48
#> 42 0.15
#> 43 0.08
#> 44 0.00
#> 45 0.00
#> 46 0.00
#### phylo_node_support_hist(): Plot a histogram of node
support values from two phylogenies
phylo_node_support_hist(
tree_ml = sauresia_ML_rooted_named,
tree_bayesian = sauresia_B_rooted_named,
bin_width = 5,
colors = c("skyblue", "green"))
#> Warning in phylo_node_support_hist(tree_ml = sauresia_ML_rooted_named,
#> tree_bayesian = sauresia_B_rooted_named, : NAs introduced by coercion
#> Warning in phylo_node_support_hist(tree_ml = sauresia_ML_rooted_named,
#> tree_bayesian = sauresia_B_rooted_named, : NAs introduced by coercion
#### phylo_heatmap(): Plot a heatmap of phylogenetic
relatedness for all individuals in a phylogeny
#### phylo_highlight_taxa(): Plot multiple phylogenies
side-by-side highlighting important taxa and nodes
phylo_highlight_taxa(
trees = list(sauresia_ML_rooted_named, sauresia_B_rooted_named),
taxa_to_highlight = c("sepsoides", "Grande Cayemite"),
highlight_colors = c("green", "orange"),
node_support_threshold = 95,
support_color = "blue",
highlight_shape = "circle",
shape_size = 1,
tip_label_size = 0.8)
#> Warning in which(as.numeric(tree$node.label) >= node_support_threshold): NAs
#> introduced by coercion
#> Warning in which(as.numeric(tree$node.label) >= node_support_threshold): NAs
#> introduced by coercion
#### phylo_plot_trees(): Plot multiple phylogenies
side-by-side with customization options including the ability to color
support values based on significance
phylo_plot_trees(
trees = list(sauresia_ML_rooted_named, sauresia_B_rooted_named, sauresia_T_named),
methods = c("ML", "Bayesian", "Time Tree"),
show_bootstraps = T,
bootstrap_color = "colored",
show_posterior = T,
posterior_color = "colored",
time_scale = T,
side_by_side = T,
name_data = new_names,
phylogeny_type = "phylogram",
edge_color = "blue")
#### Plot a phylogeny with support values from multiple trees painted on
the nodes ##### 1. phylo_node_table(): Create tables of
node values from the phylogenies
# Create and store ML node table
ML_node_table <- phylo_node_table(
sauresia_ML_rooted_named,
"ML")
#> Warning in phylo_node_table(sauresia_ML_rooted_named, "ML"): NAs introduced by
#> coercion
#> Node
#> 1 49
#> 2 50
#> 3 51
#> 4 52
#> 5 53
#> 6 54
#> 7 55
#> 8 56
#> 9 57
#> 10 58
#> 11 59
#> 12 60
#> 13 61
#> 14 62
#> 15 63
#> 16 64
#> 17 65
#> 18 66
#> 19 67
#> 20 68
#> 21 69
#> 22 70
#> 23 71
#> 24 72
#> 25 73
#> 26 74
#> 27 75
#> 28 76
#> 29 77
#> 30 78
#> 31 79
#> 32 80
#> 33 81
#> 34 82
#> 35 83
#> 36 84
#> 37 85
#> 38 86
#> 39 87
#> 40 88
#> 41 89
#> 42 90
#> 43 91
#> 44 92
#> 45 93
#> 46 94
#> 47 95
#> Taxa
#> 1 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2, Wetmorena surda 1
#> 2 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 3 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1
#> 4 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 5 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 6 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 7 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 8 Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25
#> 9 Sauresia sepsoides 3, Sauresia sepsoides 25
#> 10 Sauresia sepsoides 26, Sauresia sepsoides 27
#> 11 Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 12 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10
#> 13 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 14 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 15 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17
#> 16 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 17 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20
#> 18 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14
#> 19 Sauresia sepsoides 5, Sauresia sepsoides 7
#> 20 Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16
#> 21 Sauresia sepsoides 8, Sauresia sepsoides 16
#> 22 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 23 Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 24 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 25 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 26 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 27 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 28 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12
#> 29 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 30 Sauresia sepsoides 13, Sauresia sepsoides 21
#> 31 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 32 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2
#> 33 Sauresia manicula 1, Sauresia manicula 2
#> 34 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 35 Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 36 Sauresia agramma 3, Sauresia agramma 4
#> 37 Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 38 Sauresia pangnolae 1, Sauresia pangnolae 4
#> 39 Sauresia pangnolae 2, Sauresia pangnolae 3
#> 40 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> 41 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 42 Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 43 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 44 Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5
#> 45 Sauresia cayemitae 4, Sauresia cayemitae 6
#> 46 Sauresia habichi 1, Sauresia habichi 2
#> 47 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 9, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23, Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21, Sauresia sepsoides 12, Sauresia sepsoides 10, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 6, Sauresia cayemitae 5, Sauresia habichi 1, Sauresia habichi 2
#> Support_or_Time
#> 1 NA
#> 2 57
#> 3 68
#> 4 99
#> 5 99
#> 6 100
#> 7 58
#> 8 20
#> 9 22
#> 10 36
#> 11 80
#> 12 99
#> 13 35
#> 14 14
#> 15 11
#> 16 16
#> 17 18
#> 18 86
#> 19 96
#> 20 70
#> 21 41
#> 22 23
#> 23 38
#> 24 37
#> 25 77
#> 26 36
#> 27 95
#> 28 72
#> 29 69
#> 30 79
#> 31 94
#> 32 99
#> 33 99
#> 34 99
#> 35 72
#> 36 65
#> 37 100
#> 38 90
#> 39 79
#> 40 93
#> 41 99
#> 42 78
#> 43 93
#> 44 74
#> 45 86
#> 46 97
#> 47 NA
# Create and store Bayesian node table
bayesian_node_table <- phylo_node_table(
sauresia_B_rooted_named,
"Bayesian")
#> Warning in phylo_node_table(sauresia_B_rooted_named, "Bayesian"): NAs
#> introduced by coercion
#> Node
#> 1 49
#> 2 50
#> 3 51
#> 4 52
#> 5 53
#> 6 54
#> 7 55
#> 8 56
#> 9 57
#> 10 58
#> 11 59
#> 12 60
#> 13 61
#> 14 62
#> 15 63
#> 16 64
#> 17 65
#> 18 66
#> 19 67
#> 20 68
#> 21 69
#> 22 70
#> 23 71
#> 24 72
#> 25 73
#> 26 74
#> 27 75
#> 28 76
#> 29 77
#> 30 78
#> 31 79
#> 32 80
#> 33 81
#> 34 82
#> 35 83
#> 36 84
#> 37 85
#> 38 86
#> 39 87
#> 40 88
#> 41 89
#> 42 90
#> 43 91
#> 44 92
#> 45 93
#> 46 94
#> 47 95
#> Taxa
#> 1 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia habichi 1, Sauresia habichi 2, Wetmorena surda 1
#> 2 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 3 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1
#> 4 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 5 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24
#> 6 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27
#> 7 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26
#> 8 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25
#> 9 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3
#> 10 Sauresia sepsoides 1, Sauresia sepsoides 2
#> 11 Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24
#> 12 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24
#> 13 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23
#> 14 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21
#> 15 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20
#> 16 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22
#> 17 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17
#> 18 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16
#> 19 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18
#> 20 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13
#> 21 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12
#> 22 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11
#> 23 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10
#> 24 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 25 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8
#> 26 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6
#> 27 Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14
#> 28 Sauresia sepsoides 5, Sauresia sepsoides 7
#> 29 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 30 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 31 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 32 Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2
#> 33 Sauresia manicula 1, Sauresia manicula 2
#> 34 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 35 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3
#> 36 Sauresia agramma 1, Sauresia agramma 2
#> 37 Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3
#> 38 Sauresia pangnolae 1, Sauresia pangnolae 4
#> 39 Sauresia pangnolae 2, Sauresia pangnolae 3
#> 40 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia habichi 1, Sauresia habichi 2
#> 41 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 42 Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 43 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 44 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5
#> 45 Sauresia cayemitae 3, Sauresia cayemitae 4
#> 46 Sauresia habichi 1, Sauresia habichi 2
#> 47 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 7, Sauresia sepsoides 14, Sauresia sepsoides 6, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia synoria 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia pangnolae 1, Sauresia pangnolae 4, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia habichi 1, Sauresia habichi 2
#> Support_or_Time
#> 1 NA
#> 2 65
#> 3 75
#> 4 100
#> 5 100
#> 6 100
#> 7 0
#> 8 0
#> 9 0
#> 10 0
#> 11 60
#> 12 96
#> 13 0
#> 14 0
#> 15 0
#> 16 0
#> 17 0
#> 18 0
#> 19 0
#> 20 0
#> 21 0
#> 22 0
#> 23 0
#> 24 0
#> 25 0
#> 26 0
#> 27 60
#> 28 100
#> 29 77
#> 30 74
#> 31 100
#> 32 100
#> 33 100
#> 34 100
#> 35 0
#> 36 0
#> 37 100
#> 38 97
#> 39 93
#> 40 100
#> 41 100
#> 42 78
#> 43 100
#> 44 0
#> 45 0
#> 46 100
#> 47 NA2. phylo_merge_nodes(): Merge the node tables based on
matching taxa
merged_table <- phylo_merge_nodes(
ML_node_table,
bayesian_node_table)
#> Taxa
#> 1 Sauresia agramma 1, Sauresia agramma 2
#> 2 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3
#> 3 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 4 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia gracilis 1, Sauresia habichi 1, Sauresia habichi 2, Sauresia manicula 1, Sauresia manicula 2, Sauresia pangnolae 1, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia pangnolae 4, Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia synoria 1
#> 5 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia gracilis 1, Sauresia habichi 1, Sauresia habichi 2, Sauresia manicula 1, Sauresia manicula 2, Sauresia pangnolae 1, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia pangnolae 4, Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia synoria 1, Wetmorena surda 1
#> 6 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia pangnolae 1, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia pangnolae 4, Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia synoria 1
#> 7 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia gracilis 1, Sauresia manicula 1, Sauresia manicula 2, Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia synoria 1
#> 8 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia manicula 1, Sauresia manicula 2, Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9, Sauresia synoria 1
#> 9 Sauresia agramma 1, Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4, Sauresia manicula 1, Sauresia manicula 2, Sauresia synoria 1
#> 10 Sauresia agramma 2, Sauresia agramma 3, Sauresia agramma 4
#> 11 Sauresia agramma 3, Sauresia agramma 4
#> 12 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 13 Sauresia cayemitae 1, Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6, Sauresia habichi 1, Sauresia habichi 2
#> 14 Sauresia cayemitae 2, Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 15 Sauresia cayemitae 3, Sauresia cayemitae 4
#> 16 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5
#> 17 Sauresia cayemitae 3, Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 18 Sauresia cayemitae 4, Sauresia cayemitae 5, Sauresia cayemitae 6
#> 19 Sauresia cayemitae 4, Sauresia cayemitae 6
#> 20 Sauresia habichi 1, Sauresia habichi 2
#> 21 Sauresia manicula 1, Sauresia manicula 2
#> 22 Sauresia manicula 1, Sauresia manicula 2, Sauresia synoria 1
#> 23 Sauresia pangnolae 1, Sauresia pangnolae 2, Sauresia pangnolae 3, Sauresia pangnolae 4
#> 24 Sauresia pangnolae 1, Sauresia pangnolae 4
#> 25 Sauresia pangnolae 2, Sauresia pangnolae 3
#> 26 Sauresia sepsoides 1, Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 2, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 27 Sauresia sepsoides 1, Sauresia sepsoides 2
#> 28 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3
#> 29 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 3
#> 30 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 25, Sauresia sepsoides 3
#> 31 Sauresia sepsoides 1, Sauresia sepsoides 2, Sauresia sepsoides 3
#> 32 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 4, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 33 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 34 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 35 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 36 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 22, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 37 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 38 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 39 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 18, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 40 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 41 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 42 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 43 Sauresia sepsoides 10, Sauresia sepsoides 11, Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 44 Sauresia sepsoides 10, Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 45 Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 21, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 46 Sauresia sepsoides 11, Sauresia sepsoides 12, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 47 Sauresia sepsoides 11, Sauresia sepsoides 13, Sauresia sepsoides 21
#> 48 Sauresia sepsoides 13, Sauresia sepsoides 21
#> 49 Sauresia sepsoides 14, Sauresia sepsoides 15, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 20, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 50 Sauresia sepsoides 14, Sauresia sepsoides 16, Sauresia sepsoides 17, Sauresia sepsoides 20, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8
#> 51 Sauresia sepsoides 14, Sauresia sepsoides 16, Sauresia sepsoides 20, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8
#> 52 Sauresia sepsoides 14, Sauresia sepsoides 20, Sauresia sepsoides 5, Sauresia sepsoides 7
#> 53 Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7
#> 54 Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8
#> 55 Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 6, Sauresia sepsoides 7, Sauresia sepsoides 8, Sauresia sepsoides 9
#> 56 Sauresia sepsoides 14, Sauresia sepsoides 5, Sauresia sepsoides 7
#> 57 Sauresia sepsoides 15, Sauresia sepsoides 18
#> 58 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 23, Sauresia sepsoides 24, Sauresia sepsoides 9
#> 59 Sauresia sepsoides 15, Sauresia sepsoides 18, Sauresia sepsoides 23
#> 60 Sauresia sepsoides 16, Sauresia sepsoides 6, Sauresia sepsoides 8
#> 61 Sauresia sepsoides 16, Sauresia sepsoides 8
#> 62 Sauresia sepsoides 19, Sauresia sepsoides 22
#> 63 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24
#> 64 Sauresia sepsoides 19, Sauresia sepsoides 22, Sauresia sepsoides 24, Sauresia sepsoides 9
#> 65 Sauresia sepsoides 2, Sauresia sepsoides 25, Sauresia sepsoides 26, Sauresia sepsoides 27, Sauresia sepsoides 3
#> 66 Sauresia sepsoides 2, Sauresia sepsoides 25, Sauresia sepsoides 3
#> 67 Sauresia sepsoides 25, Sauresia sepsoides 3
#> 68 Sauresia sepsoides 26, Sauresia sepsoides 27
#> 69 Sauresia sepsoides 5, Sauresia sepsoides 7
#> Node_ML Node_Bayesian Support_Values
#> 1 NA 84 NA/0
#> 2 NA 83 NA/0
#> 3 82 82 99/100
#> 4 95 95 NA/NA
#> 5 49 49 NA/NA
#> 6 50 50 57/65
#> 7 51 51 68/75
#> 8 52 52 99/100
#> 9 79 79 94/100
#> 10 83 NA 72/NA
#> 11 84 NA 65/NA
#> 12 89 89 99/100
#> 13 88 88 93/100
#> 14 90 90 78/78
#> 15 NA 93 NA/0
#> 16 NA 92 NA/0
#> 17 91 91 93/100
#> 18 92 NA 74/NA
#> 19 93 NA 86/NA
#> 20 94 94 97/100
#> 21 81 81 99/100
#> 22 80 80 99/100
#> 23 85 85 100/100
#> 24 86 86 90/97
#> 25 87 87 79/93
#> 26 53 53 99/100
#> 27 NA 58 NA/0
#> 28 54 54 100/100
#> 29 NA 55 NA/0
#> 30 NA 56 NA/0
#> 31 NA 57 NA/0
#> 32 59 59 80/60
#> 33 60 60 99/96
#> 34 NA 61 NA/0
#> 35 NA 62 NA/0
#> 36 NA 63 NA/0
#> 37 NA 64 NA/0
#> 38 NA 65 NA/0
#> 39 NA 66 NA/0
#> 40 NA 67 NA/0
#> 41 NA 68 NA/0
#> 42 NA 69 NA/0
#> 43 NA 70 NA/0
#> 44 NA 71 NA/0
#> 45 61 NA 35/NA
#> 46 76 NA 72/NA
#> 47 77 NA 69/NA
#> 48 78 NA 79/NA
#> 49 62 NA 14/NA
#> 50 63 NA 11/NA
#> 51 64 NA 16/NA
#> 52 65 NA 18/NA
#> 53 NA 74 NA/0
#> 54 NA 73 NA/0
#> 55 NA 72 NA/0
#> 56 66 75 86/60
#> 57 75 77 95/77
#> 58 70 NA 23/NA
#> 59 74 NA 36/NA
#> 60 68 NA 70/NA
#> 61 69 NA 41/NA
#> 62 73 78 77/74
#> 63 72 NA 37/NA
#> 64 71 NA 38/NA
#> 65 55 NA 58/NA
#> 66 56 NA 20/NA
#> 67 57 NA 22/NA
#> 68 58 NA 36/NA
#> 69 67 76 96/1003. phylo_plot_tree_nodes(): Plot a tree and paint on
the merged values from merged_table
phylo_plot_tree_nodes(
tree = sauresia_ML_rooted_named,
tree_type = "ML",
merged_table = merged_table)
### 7. Documentation Functions ####
document_get_taxonomy(): Check the NCBI database for
information on a taxon
document_get_taxonomy("Sauresia sepsoides")
#> species no rank superkingdom
#> "Sauresia sepsoides" "cellular organisms" "Eukaryota"
#> clade kingdom clade
#> "Opisthokonta" "Metazoa" "Eumetazoa"
#> clade clade phylum
#> "Bilateria" "Deuterostomia" "Chordata"
#> subphylum clade clade
#> "Craniata" "Vertebrata" "Gnathostomata"
#> clade clade superclass
#> "Teleostomi" "Euteleostomi" "Sarcopterygii"
#> clade clade clade
#> "Dipnotetrapodomorpha" "Tetrapoda" "Amniota"
#> clade clade class
#> "Sauropsida" "Sauria" "Lepidosauria"
#> order clade clade
#> "Squamata" "Bifurcata" "Unidentata"
#> clade clade infraorder
#> "Episquamata" "Toxicofera" "Anguimorpha"
#> family genus
#> "Diploglossidae" "Sauresia"document_material_examined(): Create a
Materials Examined section for each group
document_material_examined(
sauresia_morpho3,
grouped_by = "Species",
region_col = "Province",
institution_col = "Museum",
number_col = "Number",
collector_col = "Collectors",
locality_col = "Locality",
date_collected_col = "Date Collected",
type_col = "Type",
sex_col = "Sex",
lat_col = "Latitude",
long_col = "Longitude",
elevation_col = "Elevation")
#> Warning in document_material_examined(sauresia_morpho3, grouped_by = "Species",
#> : The following columns are missing from the data and will be filled with
#> 'N/A': Sex
#> Material examined: Sauresia agramma (n=4).N/A. ANSP 38686 (Paratype), N/A, N/A, N/A, N/A;N/A, N/A, N/Am. ANSP 38687 (Paratype), N/A, N/A, N/A, N/A;N/A, N/A, N/Am. ANSP 38688 (Holotype), N/A, N/A, N/A, N/A;N/A, N/A, N/Am. Sud-Est. ANSP 38685 (Paratype), N/A, N/A, Morne D'Enfer, N/A; 18.330052, -72.37095, 1433m.
#>
#> Material examined: Sauresia cayemitae (n=6). Dept. de la Grand'Anse. ANSP 38691 (N/A), N/A, Richard Thomas and Manuel Leal, Pestel 5.0 km S of, N/A; 18.513286, -73.784632, 300m. Grand'Anse. ANSP 38673 (N/A), N/A, N/A, Grande Cayemite (helipad-camp), N/A; 18.63316, -73.755241, 74m. ANSP 38674 (N/A), N/A, N/A, Grande Cayemite (waypoint 166), N/A; 18.635615, -73.751749, 38m. ANSP 38675 (N/A), N/A, N/A, Grande Cayemite (waypoint 166), N/A; 18.635615, -73.751749, 38m. SBH 274212 (Paratype), N/A, N/A, Grande Cayemite (waypoint 166), N/A; 18.635615, -73.751749, 38m. ANSP 38676 (N/A), N/A, N/A, Grande Cayemite (waypoint 166), N/A; 18.635615, -73.751749, 38m.
#>
#> Material examined: Sauresia gracilis (n=1). Dept. du Sud. UNSM 328852 (Holotype), N/A, S. Blair Hedges and Richard Thomas, Port Salut 10.3 km NW, N/A; 18.140859, -73.967801, 10m.
#>
#> Material examined: Sauresia habichi (n=2). Dept. de la Grand'Anse. ANSP 38681 (Paratype), N/A, S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer, Marche Leon 8.0 km S of, N/A; 18.516777, -74.083109, 435m. ANSP 38683 (Holotype), N/A, S. Blair Hedges Manuel Leal Richard Thomas and Nicholas Plummer, Marche Leon 8.0 km S of, N/A; 18.516777, -74.083109, 435m.
#>
#> Material examined: Sauresia manicula (n=2). L'Ouest. ANSP 38667 (Holotype), N/A, N/A, Berry, N/A; 18.307945, -72.253894, 1630m. ANSP 38668 (Paratype), N/A, N/A, Berry, N/A; 18.307945, -72.253894, 1630m.
#>
#> Material examined: Sauresia pangnolae (n=4). Dept. de la Grand'Anse. ANSP 38690 (Paratype), N/A, Richard Thomas and Manuel Leal, Pestel 11.8 km S of, N/A; 18.479421, -73.78744, 550m. ANSP 38663 (Paratype), N/A, S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals, Baraderes 8.0 km SSW of, N/A; 18.44032, -73.667556, 420m. ANSP 38664 (Paratype), N/A, S. Blair Hedges Nicholas Plummer Manuel Leal Richard Thomas and locals, Baraderes 8.0 km SSW of, N/A; 18.44032, -73.667556, 420m. Nippes. ANSP 38684 (Holotype), N/A, N/A, Morne Bois Pangnol, N/A; 18.418689, -73.775122, 1170m.
#>
#> Material examined: Sauresia sepsoides (n=27). Duarte Prov.. ANSP 38666 (Paratype), N/A, Richard Thomas Manuel Leal and Herman Dominicia, Batez Piedra on west side of Rio Pazabo, N/A; 19.06997, -69.90815, 35m. SBH 193149 (N/A), N/A, Herman Dominicia Richard Thomas, Southern slopes of Loma Quita Espuela, N/A;N/A, N/A, 775m. Hato Mayor. UNSM 328846 (N/A), N/A, S. Blair Hedges and Richard Thomas, Sabana De La Mar 9.5 km W (airline) in Los Haitises, N/A; 19.05293, -69.47899, N/Am. UNSM 328850 (N/A), N/A, S. Blair Hedges and Richard Thomas, El Valle ca 15 km W (on road to Trepada Alta), N/A;N/A, N/A, N/Am. UNSM 328851 (N/A), N/A, S. Blair Hedges and Richard Thomas, El Valle ca 15 km W (on road to Trepada Alta), N/A;N/A, N/A, N/Am. SBH 267773 (N/A), N/A, RT EF and SBH, 14.1 km W El Valle; Lat: 19d0.393' N Long: 69d29.333' W, N/A;N/A, N/A, 193m. La Altagracia. ANSP 38678 (Paratype), N/A, S. Blair Hedges Richard Thomas and Nicholas Plummer, La Zanga 7.5 km W of (at Rio Maimon), N/A;N/A, N/A, 25m. Los Tabucos. ANSP 38706 (Paratype), N/A, Richard Thomas, Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.), N/A;N/A, N/A, 455m. ANSP 38707 (Paratype), N/A, Richard Thomas, Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.), N/A;N/A, N/A, 455m. ANSP 38708 (Paratype), N/A, Richard Thomas, Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.), N/A;N/A, N/A, 455m. ANSP 38709 (Paratype), N/A, Richard Thomas, Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.), N/A;N/A, N/A, 455m. Monte Plata. SBH 266746 (N/A), N/A, Richard Thomas, Los Limones footpath N of town, N/A;N/A, N/A, 197m. SBH 266748 (N/A), N/A, Richard Thomas, Los Limones 3km S, N/A;N/A, N/A, 275m. SBH 266749 (N/A), N/A, Richard Thomas, Los Limones 3km S, N/A;N/A, N/A, 275m. SBH 266750 (N/A), N/A, Richard Thomas, Los Limones 3km S, N/A;N/A, N/A, 275m. SBH 266754 (N/A), N/A, Richard Thomas, 6km S Los Limones, N/A;N/A, N/A, 305m. SBH 267754 (N/A), N/A, RT, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W, N/A; 19.01932, -69.73766, 250m. SBH 267755 (N/A), N/A, RT, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W, N/A; 19.01932, -69.73766, 250m. SBH 267756 (N/A), N/A, RT, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W, N/A; 19.01932, -69.73766, 250m. SBH 267757 (N/A), N/A, RT, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W, N/A; 19.01932, -69.73766, 250m. SBH 267758 (N/A), N/A, RT, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W, N/A; 19.01932, -69.73766, 250m. Monte Plata Prov.. ANSP 38680 (Paratype), N/A, Richard Thomas, Majagual 4.3 km N of, N/A; 19.07539, -69.82842, 90m. Parque Nacional Los Haitises. SBH 267780 (N/A), N/A, N/A, 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W, N/A; 19.06667, -69.57127, 150m. SBH 267781 (N/A), N/A, N/A, 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W, N/A; 19.06667, -69.57127, 150m. Sanchez Ramirez Prov.. ANSP 38670 (Paratype), N/A, Manuel Leal Richard Thomas, Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate), N/A; 19.1037, -70.0531, 35m. ANSP 38671 (Paratype), N/A, Manuel Leal Richard Thomas, Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate), N/A; 19.1037, -70.0531, 35m. ANSP 38672 (Paratype), N/A, Manuel Leal Richard Thomas, Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate), N/A; 19.1037, -70.0531, 35m.
#>
#> Material examined: Sauresia synoria (n=1). Pedernales. SBH 160343 (Paratype), N/A, Richard Thomas and S. Blair Hedges, Pedernales 22 km N at Rio Mulito, N/A; 18.1544, -71.7581, 274m.
#>
#> Material examined: Wetmorena surda (n=1). Pedernales. SBH 266705 (N/A), N/A, N/A, N Los Arroyos, N/A; 18.2579, -71.7446, 1660m.document_description_section(): Create a
Description section for each group
document_description_section(
sauresia_morpho3,
trait_columns = c("SVL", "Pattern", "Head Markings", "Nuchal Lines", "Dots in Lateral Band",
"Mental to Vent Scale Count", "Midbody ScaleCount", "Total Finger Lamella",
"Strigae on Ten Scales", "Total Toe Length", "Scale Under Eye to Lip Distance",
"Eye Length", "Arm Length", "Ear Width", "Rostral Width", "Rostral Height",
"Head Length", "Mental Width", "Post Mental Width", "Cloaca Width",
"Prefrontal Width", "Largest Supraoccular Width", "Finger III Length",
"Ear to Eye Distance", "Head Width", "Frontal Width", "Frontal Length"),
grouped_by = "Species")
#> Members of Sauresia agramma have (1) SVL, 49.4-69.1, (2) Pattern, 0-1, (3) Head Markings, 0-1, (4) Nuchal Lines, 0, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 121-127, (7) Midbody ScaleCount, 37-39, (8) Total Finger Lamella, 17, (9) Strigae on Ten Scales, 103-138, (10) Total Toe Length, 7.8-8.04, (11) Scale Under Eye to Lip Distance, 0.14-0.17, (12) Eye Length, 1.49-1.7, (13) Arm Length, 7.06-7.31, (14) Ear Width, 0.31-0.49, (15) Rostral Width, 1.5-1.57, (16) Rostral Height, 0.74-0.78, (17) Head Length, 8.2-9.42, (18) Mental Width, 1.04-1.11, (19) Post Mental Width, 1.45-1.62, (20) Cloaca Width, 3.67-4.21, (21) Prefrontal Width, 2.09-2.16, (22) Largest Supraoccular Width, 1.23-1.33, (23) Finger III Length, 1.46-1.54, (24) Ear to Eye Distance, 4.23-4.79, (25) Head Width, 6.12-6.77, (26) Frontal Width, 2.31-2.55, and (27) Frontal Length, 2.82-3.18.
#>
#> Members of Sauresia cayemitae have (1) SVL, 47.8-58.1, (2) Pattern, 2-5, (3) Head Markings, 1, (4) Nuchal Lines, 1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 110-117, (7) Midbody ScaleCount, 32-37, (8) Total Finger Lamella, 16-19, (9) Strigae on Ten Scales, 84-104, (10) Total Toe Length, 5.69-7.8, (11) Scale Under Eye to Lip Distance, 0.03-0.14, (12) Eye Length, 1.27-1.57, (13) Arm Length, 5.49-7.29, (14) Ear Width, 0.41-0.63, (15) Rostral Width, 1.16-1.41, (16) Rostral Height, 0.51-0.8, (17) Head Length, 6.61-8.87, (18) Mental Width, 0.77-0.96, (19) Post Mental Width, 1.15-1.42, (20) Cloaca Width, 2.67-3.54, (21) Prefrontal Width, 1.66-2.01, (22) Largest Supraoccular Width, 0.97-1.2, (23) Finger III Length, 1.13-1.54, (24) Ear to Eye Distance, 2.97-3.87, (25) Head Width, 5.02-6.08, (26) Frontal Width, 1.63-2.06, and (27) Frontal Length, 2.23-2.82.
#>
#> Members of Sauresia gracilis have (1) SVL, 51.1, (2) Pattern, N/A, (3) Head Markings, 1, (4) Nuchal Lines, 1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 103, (7) Midbody ScaleCount, 36, (8) Total Finger Lamella, 18, (9) Strigae on Ten Scales, 100, (10) Total Toe Length, 7.07, (11) Scale Under Eye to Lip Distance, 0.13, (12) Eye Length, 1.52, (13) Arm Length, 5.54, (14) Ear Width, 0.34, (15) Rostral Width, 1.33, (16) Rostral Height, 0.7, (17) Head Length, 8.03, (18) Mental Width, 0.9, (19) Post Mental Width, 1.41, (20) Cloaca Width, 3.67, (21) Prefrontal Width, 1.95, (22) Largest Supraoccular Width, 1.25, (23) Finger III Length, 1, (24) Ear to Eye Distance, 3.9, (25) Head Width, 5.43, (26) Frontal Width, 2.03, and (27) Frontal Length, 2.45.
#>
#> Members of Sauresia habichi have (1) SVL, 50.5-59.7, (2) Pattern, 3-5, (3) Head Markings, 1, (4) Nuchal Lines, 1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 122-125, (7) Midbody ScaleCount, 38-41, (8) Total Finger Lamella, 18-19, (9) Strigae on Ten Scales, 89-113, (10) Total Toe Length, 6.63-7.72, (11) Scale Under Eye to Lip Distance, 0.03-0.12, (12) Eye Length, 1.21-1.38, (13) Arm Length, 6.61-7.04, (14) Ear Width, 0.34-0.38, (15) Rostral Width, 1.43-1.46, (16) Rostral Height, 0.59-0.8, (17) Head Length, 7.16-8.94, (18) Mental Width, 0.92-0.93, (19) Post Mental Width, 1.18-1.39, (20) Cloaca Width, 3.07-3.99, (21) Prefrontal Width, 2-2.25, (22) Largest Supraoccular Width, 1.05-1.33, (23) Finger III Length, 1.37-1.4, (24) Ear to Eye Distance, 3.41-4.36, (25) Head Width, 5.63-6.95, (26) Frontal Width, 1.88-2.14, and (27) Frontal Length, 2.54-2.98.
#>
#> Members of Sauresia manicula have (1) SVL, 59.6-69, (2) Pattern, 3, (3) Head Markings, N/A, (4) Nuchal Lines, 1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 123-129, (7) Midbody ScaleCount, 37, (8) Total Finger Lamella, 17, (9) Strigae on Ten Scales, 119-150, (10) Total Toe Length, 6.68-8.32, (11) Scale Under Eye to Lip Distance, 0.1-0.13, (12) Eye Length, 1.38-1.58, (13) Arm Length, 7.09-7.93, (14) Ear Width, 0.36-0.6, (15) Rostral Width, 1.36-1.73, (16) Rostral Height, 0.72-0.91, (17) Head Length, 7.78-9.83, (18) Mental Width, 0.88-1.15, (19) Post Mental Width, 1.27-1.49, (20) Cloaca Width, 3.16-4.42, (21) Prefrontal Width, 1.98-2.5, (22) Largest Supraoccular Width, 1.11-1.39, (23) Finger III Length, 1.32-1.52, (24) Ear to Eye Distance, 4.03-5.17, (25) Head Width, 5.67-8.14, (26) Frontal Width, 2.55, and (27) Frontal Length, 2.59-3.13.
#>
#> Members of Sauresia pangnolae have (1) SVL, 54.3-66.7, (2) Pattern, 1-2, (3) Head Markings, 0, (4) Nuchal Lines, 0-1, (5) Dots in Lateral Band, 1, (6) Mental to Vent Scale Count, 104-115, (7) Midbody ScaleCount, 38-42, (8) Total Finger Lamella, 15-19, (9) Strigae on Ten Scales, 92-109, (10) Total Toe Length, 7.42-8.82, (11) Scale Under Eye to Lip Distance, 0.07-0.12, (12) Eye Length, 1.51-1.93, (13) Arm Length, 6.78-7.95, (14) Ear Width, 0.44-0.61, (15) Rostral Width, 1.38-1.94, (16) Rostral Height, 0.76-0.94, (17) Head Length, 8.3-10.1, (18) Mental Width, 0.79-1.27, (19) Post Mental Width, 1.11-1.65, (20) Cloaca Width, 3.66-4.2, (21) Prefrontal Width, 2.01-2.47, (22) Largest Supraoccular Width, 1.15-1.49, (23) Finger III Length, 1.38-1.53, (24) Ear to Eye Distance, 4.04-4.97, (25) Head Width, 6.24-7.15, (26) Frontal Width, 2.06-2.74, and (27) Frontal Length, 2.6-3.6.
#>
#> Members of Sauresia sepsoides have (1) SVL, 32.8-65.2, (2) Pattern, 1-2, (3) Head Markings, 0-1, (4) Nuchal Lines, 0-1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 108-119, (7) Midbody ScaleCount, 35-37, (8) Total Finger Lamella, 14-17, (9) Strigae on Ten Scales, 94-114, (10) Total Toe Length, 6.35-8.24, (11) Scale Under Eye to Lip Distance, 0.11-0.19, (12) Eye Length, 1.36-1.62, (13) Arm Length, 5.81-7.01, (14) Ear Width, 0.3-0.59, (15) Rostral Width, 1.45-2, (16) Rostral Height, 0.66-1, (17) Head Length, 7.34-9.28, (18) Mental Width, 0.78-1.11, (19) Post Mental Width, 1.12-1.43, (20) Cloaca Width, 3.01-4.06, (21) Prefrontal Width, 1.98-2.36, (22) Largest Supraoccular Width, 1-1.41, (23) Finger III Length, 1.03-1.38, (24) Ear to Eye Distance, 3.75-4.77, (25) Head Width, 5.2-6.79, (26) Frontal Width, 2.04-2.35, and (27) Frontal Length, 2.57-3.27.
#>
#> Members of Sauresia synoria have (1) SVL, 63.7, (2) Pattern, 0, (3) Head Markings, 1, (4) Nuchal Lines, 1, (5) Dots in Lateral Band, 0, (6) Mental to Vent Scale Count, 123, (7) Midbody ScaleCount, 34, (8) Total Finger Lamella, 18, (9) Strigae on Ten Scales, 111, (10) Total Toe Length, 6.68, (11) Scale Under Eye to Lip Distance, 0.2, (12) Eye Length, 1.57, (13) Arm Length, 5.82, (14) Ear Width, 0.39, (15) Rostral Width, 1.53, (16) Rostral Height, 0.84, (17) Head Length, 7.8, (18) Mental Width, 0.77, (19) Post Mental Width, 1.54, (20) Cloaca Width, 3.58, (21) Prefrontal Width, 2.04, (22) Largest Supraoccular Width, 1.06, (23) Finger III Length, 1.46, (24) Ear to Eye Distance, 3.76, (25) Head Width, 5.93, (26) Frontal Width, N/A, and (27) Frontal Length, 2.37.
#>
#> Members of Wetmorena surda have (1) SVL, N/A, (2) Pattern, N/A, (3) Head Markings, N/A, (4) Nuchal Lines, N/A, (5) Dots in Lateral Band, N/A, (6) Mental to Vent Scale Count, N/A, (7) Midbody ScaleCount, N/A, (8) Total Finger Lamella, N/A, (9) Strigae on Ten Scales, N/A, (10) Total Toe Length, N/A, (11) Scale Under Eye to Lip Distance, N/A, (12) Eye Length, N/A, (13) Arm Length, N/A, (14) Ear Width, N/A, (15) Rostral Width, N/A, (16) Rostral Height, N/A, (17) Head Length, N/A, (18) Mental Width, N/A, (19) Post Mental Width, N/A, (20) Cloaca Width, N/A, (21) Prefrontal Width, N/A, (22) Largest Supraoccular Width, N/A, (23) Finger III Length, N/A, (24) Ear to Eye Distance, N/A, (25) Head Width, N/A, (26) Frontal Width, N/A, and (27) Frontal Length, N/A.document_standout_traits(): Identify traits that are
different in one group compared to values in all or most other
groups
document_standout_traits(
sauresia_morpho3,
trait_columns = c("SVL", "Pattern", "Head Markings", "Nuchal Lines", "Dots in Lateral Band",
"Mental to Vent Scale Count", "Midbody ScaleCount", "Total Finger Lamella",
"Strigae on Ten Scales", "Total Toe Length", "Scale Under Eye to Lip Distance",
"Eye Length", "Arm Length", "Ear Width", "Rostral Width", "Rostral Height",
"Head Length", "Mental Width", "Post Mental Width", "Cloaca Width",
"Prefrontal Width", "Largest Supraoccular Width", "Finger III Length",
"Ear to Eye Distance", "Head Width", "Frontal Width", "Frontal Length"),
grouped_by = "Species",
cutoff = 2/3)
#> Warning: There were 60 warnings in `summarise()`.
#> The first warning was:
#> ℹ In argument: `across(...)`.
#> ℹ In group 9: `Species = "Wetmorena surda"`.
#> Caused by warning in `min()`:
#> ! no non-missing arguments to min; returning Inf
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 59 remaining warnings.
#> $range_summaries
#> # A tibble: 9 × 55
#> Species SVL_min SVL_max Pattern_min Pattern_max `Head Markings_min`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Sauresia agramma 49.4 69.1 0 1 0
#> 2 Sauresia cayemitae 47.8 58.1 2 5 1
#> 3 Sauresia gracilis 51.1 51.1 Inf -Inf 1
#> 4 Sauresia habichi 50.5 59.7 3 5 1
#> 5 Sauresia manicula 59.6 69 3 3 Inf
#> 6 Sauresia pangnolae 54.3 66.7 1 2 0
#> 7 Sauresia sepsoides 32.8 65.2 1 2 0
#> 8 Sauresia synoria 63.7 63.7 0 0 1
#> 9 Wetmorena surda Inf -Inf Inf -Inf Inf
#> # ℹ 49 more variables: `Head Markings_max` <dbl>, `Nuchal Lines_min` <dbl>,
#> # `Nuchal Lines_max` <dbl>, `Dots in Lateral Band_min` <dbl>,
#> # `Dots in Lateral Band_max` <dbl>, `Mental to Vent Scale Count_min` <dbl>,
#> # `Mental to Vent Scale Count_max` <dbl>, `Midbody ScaleCount_min` <dbl>,
#> # `Midbody ScaleCount_max` <dbl>, `Total Finger Lamella_min` <dbl>,
#> # `Total Finger Lamella_max` <dbl>, `Strigae on Ten Scales_min` <dbl>,
#> # `Strigae on Ten Scales_max` <dbl>, `Total Toe Length_min` <dbl>, …
#>
#> $diagnostic_messages
#> $diagnostic_messages[[1]]
#> [1] "Sauresia habichi has a larger range in Pattern than 75% of the other groups."
#>
#> $diagnostic_messages[[2]]
#> [1] "Sauresia manicula has a larger range in Pattern than 75% of the other groups."
#>
#> $diagnostic_messages[[3]]
#> [1] "Sauresia synoria has a smaller range in Pattern than 88% of the other groups."
#>
#> $diagnostic_messages[[4]]
#> [1] "Sauresia pangnolae has a smaller range in Head Markings than 75% of the other groups."
#>
#> $diagnostic_messages[[5]]
#> [1] "Sauresia agramma has a smaller range in Nuchal Lines than 75% of the other groups."
#>
#> $diagnostic_messages[[6]]
#> [1] "Sauresia pangnolae has a larger range in Dots in Lateral Band than 100% of the other groups."
#>
#> $diagnostic_messages[[7]]
#> [1] "Sauresia gracilis has a smaller range in Mental to Vent Scale Count than all of the other groups."
#>
#> $diagnostic_messages[[8]]
#> [1] "Sauresia habichi has a larger range in Midbody ScaleCount than 75% of the other groups."
#>
#> $diagnostic_messages[[9]]
#> [1] "Sauresia pangnolae has a larger range in Midbody ScaleCount than 75% of the other groups."
#>
#> $diagnostic_messages[[10]]
#> [1] "Sauresia synoria has a smaller range in Midbody ScaleCount than 88% of the other groups."
#>
#> $diagnostic_messages[[11]]
#> [1] "Sauresia manicula has a larger range in Strigae on Ten Scales than 88% of the other groups."
#>
#> $diagnostic_messages[[12]]
#> [1] "Sauresia synoria has a larger range in Scale Under Eye to Lip Distance than 100% of the other groups."
#>
#> $diagnostic_messages[[13]]
#> [1] "Sauresia gracilis has a smaller range in Arm Length than 88% of the other groups."
#>
#> $diagnostic_messages[[14]]
#> [1] "Sauresia gracilis has a smaller range in Rostral Width than 88% of the other groups."
#>
#> $diagnostic_messages[[15]]
#> [1] "Sauresia synoria has a smaller range in Mental Width than 88% of the other groups."
#>
#> $diagnostic_messages[[16]]
#> [1] "Sauresia synoria has a larger range in Post Mental Width than 75% of the other groups."
#>
#> $diagnostic_messages[[17]]
#> [1] "Sauresia gracilis has a smaller range in Prefrontal Width than 88% of the other groups."
#>
#> $diagnostic_messages[[18]]
#> [1] "Sauresia gracilis has a smaller range in Finger III Length than all of the other groups."
#>
#> $diagnostic_messages[[19]]
#> [1] "Sauresia gracilis has a smaller range in Head Width than 75% of the other groups."
#>
#> $diagnostic_messages[[20]]
#> [1] "Sauresia gracilis has a smaller range in Frontal Width than 75% of the other groups."
#>
#> $diagnostic_messages[[21]]
#> [1] "Sauresia manicula has a larger range in Frontal Width than 75% of the other groups."
#>
#> $diagnostic_messages[[22]]
#> [1] "Sauresia gracilis has a smaller range in Frontal Length than 75% of the other groups."
#>
#> $diagnostic_messages[[23]]
#> [1] "Sauresia synoria has a smaller range in Frontal Length than 88% of the other groups."document_diagnoses_section(): Create a
Diagnosis section for each group
document_diagnoses_section(sauresia_morpho3,
trait_columns = c("SVL", "Pattern", "Head Markings", "Nuchal Lines", "Dots in Lateral Band",
"Mental to Vent Scale Count", "Midbody ScaleCount", "Total Finger Lamella",
"Strigae on Ten Scales", "Total Toe Length", "Scale Under Eye to Lip Distance",
"Eye Length", "Arm Length", "Ear Width", "Rostral Width", "Rostral Height",
"Head Length", "Mental Width", "Post Mental Width", "Cloaca Width",
"Prefrontal Width", "Largest Supraoccular Width", "Finger III Length",
"Ear to Eye Distance", "Head Width", "Frontal Width", "Frontal Length"),
grouped_by = "Species")
#> From Sauresia agramma, we distinguish Sauresia cayemitae by Pattern (0-1 vs 2-5), Nuchal Lines (0 vs 1), Mental to Vent Scale Count (121-127 vs 110-117), Rostral Width (1.5-1.57 vs 1.16-1.41), Mental Width (1.04-1.11 vs 0.77-0.96), Post Mental Width (1.45-1.62 vs 1.15-1.42), Cloaca Width (3.67-4.21 vs 2.67-3.54), Prefrontal Width (2.09-2.16 vs 1.66-2.01), Largest Supraoccular Width (1.23-1.33 vs 0.97-1.2), Ear to Eye Distance (4.23-4.79 vs 2.97-3.87), Head Width (6.12-6.77 vs 5.02-6.08), and Frontal Width (2.31-2.55 vs 1.63-2.06).
#>
#> From Sauresia cayemitae, we distinguish Sauresia agramma by Pattern (2-5 vs 0-1), Nuchal Lines (1 vs 0), Mental to Vent Scale Count (110-117 vs 121-127), Rostral Width (1.16-1.41 vs 1.5-1.57), Mental Width (0.77-0.96 vs 1.04-1.11), Post Mental Width (1.15-1.42 vs 1.45-1.62), Cloaca Width (2.67-3.54 vs 3.67-4.21), Prefrontal Width (1.66-2.01 vs 2.09-2.16), Largest Supraoccular Width (0.97-1.2 vs 1.23-1.33), Ear to Eye Distance (2.97-3.87 vs 4.23-4.79), Head Width (5.02-6.08 vs 6.12-6.77), and Frontal Width (1.63-2.06 vs 2.31-2.55).
#>
#> From Sauresia agramma, we distinguish Sauresia gracilis by Nuchal Lines (0 vs 1), Mental to Vent Scale Count (121-127 vs 103), Midbody ScaleCount (37-39 vs 36), Total Finger Lamella (17 vs 18), Strigae on Ten Scales (103-138 vs 100), Total Toe Length (7.8-8.04 vs 7.07), Scale Under Eye to Lip Distance (0.14-0.17 vs 0.13), Arm Length (7.06-7.31 vs 5.54), Rostral Width (1.5-1.57 vs 1.33), Rostral Height (0.74-0.78 vs 0.7), Head Length (8.2-9.42 vs 8.03), Mental Width (1.04-1.11 vs 0.9), Post Mental Width (1.45-1.62 vs 1.41), Prefrontal Width (2.09-2.16 vs 1.95), Finger III Length (1.46-1.54 vs 1), Ear to Eye Distance (4.23-4.79 vs 3.9), Head Width (6.12-6.77 vs 5.43), Frontal Width (2.31-2.55 vs 2.03), and Frontal Length (2.82-3.18 vs 2.45).
#>
#> From Sauresia gracilis, we distinguish Sauresia agramma by Nuchal Lines (1 vs 0), Mental to Vent Scale Count (103 vs 121-127), Midbody ScaleCount (36 vs 37-39), Total Finger Lamella (18 vs 17), Strigae on Ten Scales (100 vs 103-138), Total Toe Length (7.07 vs 7.8-8.04), Scale Under Eye to Lip Distance (0.13 vs 0.14-0.17), Arm Length (5.54 vs 7.06-7.31), Rostral Width (1.33 vs 1.5-1.57), Rostral Height (0.7 vs 0.74-0.78), Head Length (8.03 vs 8.2-9.42), Mental Width (0.9 vs 1.04-1.11), Post Mental Width (1.41 vs 1.45-1.62), Prefrontal Width (1.95 vs 2.09-2.16), Finger III Length (1 vs 1.46-1.54), Ear to Eye Distance (3.9 vs 4.23-4.79), Head Width (5.43 vs 6.12-6.77), Frontal Width (2.03 vs 2.31-2.55), and Frontal Length (2.45 vs 2.82-3.18).
#>
#> From Sauresia agramma, we distinguish Sauresia habichi by Pattern (0-1 vs 3-5), Nuchal Lines (0 vs 1), Total Finger Lamella (17 vs 18-19), Total Toe Length (7.8-8.04 vs 6.63-7.72), Scale Under Eye to Lip Distance (0.14-0.17 vs 0.03-0.12), Eye Length (1.49-1.7 vs 1.21-1.38), Arm Length (7.06-7.31 vs 6.61-7.04), Rostral Width (1.5-1.57 vs 1.43-1.46), Mental Width (1.04-1.11 vs 0.92-0.93), Post Mental Width (1.45-1.62 vs 1.18-1.39), Finger III Length (1.46-1.54 vs 1.37-1.4), and Frontal Width (2.31-2.55 vs 1.88-2.14).
#>
#> From Sauresia habichi, we distinguish Sauresia agramma by Pattern (3-5 vs 0-1), Nuchal Lines (1 vs 0), Total Finger Lamella (18-19 vs 17), Total Toe Length (6.63-7.72 vs 7.8-8.04), Scale Under Eye to Lip Distance (0.03-0.12 vs 0.14-0.17), Eye Length (1.21-1.38 vs 1.49-1.7), Arm Length (6.61-7.04 vs 7.06-7.31), Rostral Width (1.43-1.46 vs 1.5-1.57), Mental Width (0.92-0.93 vs 1.04-1.11), Post Mental Width (1.18-1.39 vs 1.45-1.62), Finger III Length (1.37-1.4 vs 1.46-1.54), and Frontal Width (1.88-2.14 vs 2.31-2.55).
#>
#> From Sauresia agramma, we distinguish Sauresia manicula by Pattern (0-1 vs 3), Nuchal Lines (0 vs 1), and Scale Under Eye to Lip Distance (0.14-0.17 vs 0.1-0.13).
#>
#> From Sauresia manicula, we distinguish Sauresia agramma by Pattern (3 vs 0-1), Nuchal Lines (1 vs 0), and Scale Under Eye to Lip Distance (0.1-0.13 vs 0.14-0.17).
#>
#> From Sauresia agramma, we distinguish Sauresia pangnolae by Dots in Lateral Band (0 vs 1), Mental to Vent Scale Count (121-127 vs 104-115), and Scale Under Eye to Lip Distance (0.14-0.17 vs 0.07-0.12).
#>
#> From Sauresia pangnolae, we distinguish Sauresia agramma by Dots in Lateral Band (1 vs 0), Mental to Vent Scale Count (104-115 vs 121-127), and Scale Under Eye to Lip Distance (0.07-0.12 vs 0.14-0.17).
#>
#> From Sauresia agramma, we distinguish Sauresia sepsoides by Mental to Vent Scale Count (121-127 vs 108-119), Arm Length (7.06-7.31 vs 5.81-7.01), Post Mental Width (1.45-1.62 vs 1.12-1.43), and Finger III Length (1.46-1.54 vs 1.03-1.38).
#>
#> From Sauresia sepsoides, we distinguish Sauresia agramma by Mental to Vent Scale Count (108-119 vs 121-127), Arm Length (5.81-7.01 vs 7.06-7.31), Post Mental Width (1.12-1.43 vs 1.45-1.62), and Finger III Length (1.03-1.38 vs 1.46-1.54).
#>
#> From Sauresia agramma, we distinguish Sauresia synoria by Nuchal Lines (0 vs 1), Midbody ScaleCount (37-39 vs 34), Total Finger Lamella (17 vs 18), Total Toe Length (7.8-8.04 vs 6.68), Scale Under Eye to Lip Distance (0.14-0.17 vs 0.2), Arm Length (7.06-7.31 vs 5.82), Rostral Height (0.74-0.78 vs 0.84), Head Length (8.2-9.42 vs 7.8), Mental Width (1.04-1.11 vs 0.77), Cloaca Width (3.67-4.21 vs 3.58), Prefrontal Width (2.09-2.16 vs 2.04), Largest Supraoccular Width (1.23-1.33 vs 1.06), Ear to Eye Distance (4.23-4.79 vs 3.76), Head Width (6.12-6.77 vs 5.93), and Frontal Length (2.82-3.18 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia agramma by Nuchal Lines (1 vs 0), Midbody ScaleCount (34 vs 37-39), Total Finger Lamella (18 vs 17), Total Toe Length (6.68 vs 7.8-8.04), Scale Under Eye to Lip Distance (0.2 vs 0.14-0.17), Arm Length (5.82 vs 7.06-7.31), Rostral Height (0.84 vs 0.74-0.78), Head Length (7.8 vs 8.2-9.42), Mental Width (0.77 vs 1.04-1.11), Cloaca Width (3.58 vs 3.67-4.21), Prefrontal Width (2.04 vs 2.09-2.16), Largest Supraoccular Width (1.06 vs 1.23-1.33), Ear to Eye Distance (3.76 vs 4.23-4.79), Head Width (5.93 vs 6.12-6.77), and Frontal Length (2.37 vs 2.82-3.18).
#>
#> From Sauresia cayemitae, we distinguish Sauresia gracilis by Mental to Vent Scale Count (110-117 vs 103), Ear Width (0.41-0.63 vs 0.34), Cloaca Width (2.67-3.54 vs 3.67), Largest Supraoccular Width (0.97-1.2 vs 1.25), Finger III Length (1.13-1.54 vs 1), and Ear to Eye Distance (2.97-3.87 vs 3.9).
#>
#> From Sauresia gracilis, we distinguish Sauresia cayemitae by Mental to Vent Scale Count (103 vs 110-117), Ear Width (0.34 vs 0.41-0.63), Cloaca Width (3.67 vs 2.67-3.54), Largest Supraoccular Width (1.25 vs 0.97-1.2), Finger III Length (1 vs 1.13-1.54), and Ear to Eye Distance (3.9 vs 2.97-3.87).
#>
#> From Sauresia cayemitae, we distinguish Sauresia habichi by Mental to Vent Scale Count (110-117 vs 122-125), Midbody ScaleCount (32-37 vs 38-41), Ear Width (0.41-0.63 vs 0.34-0.38), and Rostral Width (1.16-1.41 vs 1.43-1.46).
#>
#> From Sauresia habichi, we distinguish Sauresia cayemitae by Mental to Vent Scale Count (122-125 vs 110-117), Midbody ScaleCount (38-41 vs 32-37), Ear Width (0.34-0.38 vs 0.41-0.63), and Rostral Width (1.43-1.46 vs 1.16-1.41).
#>
#> From Sauresia cayemitae, we distinguish Sauresia manicula by SVL (47.8-58.1 vs 59.6-69), Mental to Vent Scale Count (110-117 vs 123-129), Strigae on Ten Scales (84-104 vs 119-150), Ear to Eye Distance (2.97-3.87 vs 4.03-5.17), and Frontal Width (1.63-2.06 vs 2.55).
#>
#> From Sauresia manicula, we distinguish Sauresia cayemitae by SVL (59.6-69 vs 47.8-58.1), Mental to Vent Scale Count (123-129 vs 110-117), Strigae on Ten Scales (119-150 vs 84-104), Ear to Eye Distance (4.03-5.17 vs 2.97-3.87), and Frontal Width (2.55 vs 1.63-2.06).
#>
#> From Sauresia cayemitae, we distinguish Sauresia pangnolae by Head Markings (1 vs 0), Dots in Lateral Band (0 vs 1), Midbody ScaleCount (32-37 vs 38-42), Cloaca Width (2.67-3.54 vs 3.66-4.2), Ear to Eye Distance (2.97-3.87 vs 4.04-4.97), and Head Width (5.02-6.08 vs 6.24-7.15).
#>
#> From Sauresia pangnolae, we distinguish Sauresia cayemitae by Head Markings (0 vs 1), Dots in Lateral Band (1 vs 0), Midbody ScaleCount (38-42 vs 32-37), Cloaca Width (3.66-4.2 vs 2.67-3.54), Ear to Eye Distance (4.04-4.97 vs 2.97-3.87), and Head Width (6.24-7.15 vs 5.02-6.08).
#>
#> From Sauresia cayemitae, we distinguish Sauresia sepsoides by Rostral Width (1.16-1.41 vs 1.45-2).
#>
#> From Sauresia sepsoides, we distinguish Sauresia cayemitae by Rostral Width (1.45-2 vs 1.16-1.41).
#>
#> From Sauresia cayemitae, we distinguish Sauresia synoria by SVL (47.8-58.1 vs 63.66), Pattern (2-5 vs 0), Mental to Vent Scale Count (110-117 vs 123), Strigae on Ten Scales (84-104 vs 111), Scale Under Eye to Lip Distance (0.03-0.14 vs 0.2), Ear Width (0.41-0.63 vs 0.39), Rostral Width (1.16-1.41 vs 1.53), Rostral Height (0.51-0.8 vs 0.84), Post Mental Width (1.15-1.42 vs 1.54), Cloaca Width (2.67-3.54 vs 3.58), and Prefrontal Width (1.66-2.01 vs 2.04).
#>
#> From Sauresia synoria, we distinguish Sauresia cayemitae by SVL (63.66 vs 47.8-58.1), Pattern (0 vs 2-5), Mental to Vent Scale Count (123 vs 110-117), Strigae on Ten Scales (111 vs 84-104), Scale Under Eye to Lip Distance (0.2 vs 0.03-0.14), Ear Width (0.39 vs 0.41-0.63), Rostral Width (1.53 vs 1.16-1.41), Rostral Height (0.84 vs 0.51-0.8), Post Mental Width (1.54 vs 1.15-1.42), Cloaca Width (3.58 vs 2.67-3.54), and Prefrontal Width (2.04 vs 1.66-2.01).
#>
#> From Sauresia gracilis, we distinguish Sauresia habichi by Mental to Vent Scale Count (103 vs 122-125), Midbody ScaleCount (36 vs 38-41), Scale Under Eye to Lip Distance (0.13 vs 0.03-0.12), Eye Length (1.52 vs 1.21-1.38), Arm Length (5.54 vs 6.61-7.04), Rostral Width (1.33 vs 1.43-1.46), Mental Width (0.9 vs 0.92-0.93), Post Mental Width (1.41 vs 1.18-1.39), Prefrontal Width (1.95 vs 2-2.25), Finger III Length (1 vs 1.37-1.4), Head Width (5.43 vs 5.63-6.95), and Frontal Length (2.45 vs 2.54-2.98).
#>
#> From Sauresia habichi, we distinguish Sauresia gracilis by Mental to Vent Scale Count (122-125 vs 103), Midbody ScaleCount (38-41 vs 36), Scale Under Eye to Lip Distance (0.03-0.12 vs 0.13), Eye Length (1.21-1.38 vs 1.52), Arm Length (6.61-7.04 vs 5.54), Rostral Width (1.43-1.46 vs 1.33), Mental Width (0.92-0.93 vs 0.9), Post Mental Width (1.18-1.39 vs 1.41), Prefrontal Width (2-2.25 vs 1.95), Finger III Length (1.37-1.4 vs 1), Head Width (5.63-6.95 vs 5.43), and Frontal Length (2.54-2.98 vs 2.45).
#>
#> From Sauresia gracilis, we distinguish Sauresia manicula by SVL (51.14 vs 59.6-69), Mental to Vent Scale Count (103 vs 123-129), Midbody ScaleCount (36 vs 37), Total Finger Lamella (18 vs 17), Strigae on Ten Scales (100 vs 119-150), Arm Length (5.54 vs 7.09-7.93), Ear Width (0.34 vs 0.36-0.6), Rostral Width (1.33 vs 1.36-1.73), Rostral Height (0.7 vs 0.72-0.91), Prefrontal Width (1.95 vs 1.98-2.5), Finger III Length (1 vs 1.32-1.52), Ear to Eye Distance (3.9 vs 4.03-5.17), Head Width (5.43 vs 5.67-8.14), Frontal Width (2.03 vs 2.55), and Frontal Length (2.45 vs 2.59-3.13).
#>
#> From Sauresia manicula, we distinguish Sauresia gracilis by SVL (59.6-69 vs 51.14), Mental to Vent Scale Count (123-129 vs 103), Midbody ScaleCount (37 vs 36), Total Finger Lamella (17 vs 18), Strigae on Ten Scales (119-150 vs 100), Arm Length (7.09-7.93 vs 5.54), Ear Width (0.36-0.6 vs 0.34), Rostral Width (1.36-1.73 vs 1.33), Rostral Height (0.72-0.91 vs 0.7), Prefrontal Width (1.98-2.5 vs 1.95), Finger III Length (1.32-1.52 vs 1), Ear to Eye Distance (4.03-5.17 vs 3.9), Head Width (5.67-8.14 vs 5.43), Frontal Width (2.55 vs 2.03), and Frontal Length (2.59-3.13 vs 2.45).
#>
#> From Sauresia gracilis, we distinguish Sauresia pangnolae by SVL (51.14 vs 54.3-66.7), Head Markings (1 vs 0), Dots in Lateral Band (0 vs 1), Mental to Vent Scale Count (103 vs 104-115), Midbody ScaleCount (36 vs 38-42), Total Toe Length (7.07 vs 7.42-8.82), Scale Under Eye to Lip Distance (0.13 vs 0.07-0.12), Arm Length (5.54 vs 6.78-7.95), Ear Width (0.34 vs 0.44-0.61), Rostral Width (1.33 vs 1.38-1.94), Rostral Height (0.7 vs 0.76-0.94), Head Length (8.03 vs 8.3-10.1), Prefrontal Width (1.95 vs 2.01-2.47), Finger III Length (1 vs 1.38-1.53), Ear to Eye Distance (3.9 vs 4.04-4.97), Head Width (5.43 vs 6.24-7.15), Frontal Width (2.03 vs 2.06-2.74), and Frontal Length (2.45 vs 2.6-3.6).
#>
#> From Sauresia pangnolae, we distinguish Sauresia gracilis by SVL (54.3-66.7 vs 51.14), Head Markings (0 vs 1), Dots in Lateral Band (1 vs 0), Mental to Vent Scale Count (104-115 vs 103), Midbody ScaleCount (38-42 vs 36), Total Toe Length (7.42-8.82 vs 7.07), Scale Under Eye to Lip Distance (0.07-0.12 vs 0.13), Arm Length (6.78-7.95 vs 5.54), Ear Width (0.44-0.61 vs 0.34), Rostral Width (1.38-1.94 vs 1.33), Rostral Height (0.76-0.94 vs 0.7), Head Length (8.3-10.1 vs 8.03), Prefrontal Width (2.01-2.47 vs 1.95), Finger III Length (1.38-1.53 vs 1), Ear to Eye Distance (4.04-4.97 vs 3.9), Head Width (6.24-7.15 vs 5.43), Frontal Width (2.06-2.74 vs 2.03), and Frontal Length (2.6-3.6 vs 2.45).
#>
#> From Sauresia gracilis, we distinguish Sauresia sepsoides by Mental to Vent Scale Count (103 vs 108-119), Total Finger Lamella (18 vs 14-17), Arm Length (5.54 vs 5.81-7.01), Rostral Width (1.33 vs 1.45-2), Prefrontal Width (1.95 vs 1.98-2.36), Finger III Length (1 vs 1.03-1.38), Frontal Width (2.03 vs 2.04-2.35), and Frontal Length (2.45 vs 2.57-3.27).
#>
#> From Sauresia sepsoides, we distinguish Sauresia gracilis by Mental to Vent Scale Count (108-119 vs 103), Total Finger Lamella (14-17 vs 18), Arm Length (5.81-7.01 vs 5.54), Rostral Width (1.45-2 vs 1.33), Prefrontal Width (1.98-2.36 vs 1.95), Finger III Length (1.03-1.38 vs 1), Frontal Width (2.04-2.35 vs 2.03), and Frontal Length (2.57-3.27 vs 2.45).
#>
#> From Sauresia gracilis, we distinguish Sauresia synoria by SVL (51.14 vs 63.66), Mental to Vent Scale Count (103 vs 123), Midbody ScaleCount (36 vs 34), Strigae on Ten Scales (100 vs 111), Total Toe Length (7.07 vs 6.68), Scale Under Eye to Lip Distance (0.13 vs 0.2), Eye Length (1.52 vs 1.57), Arm Length (5.54 vs 5.82), Ear Width (0.34 vs 0.39), Rostral Width (1.33 vs 1.53), Rostral Height (0.7 vs 0.84), Head Length (8.03 vs 7.8), Mental Width (0.9 vs 0.77), Post Mental Width (1.41 vs 1.54), Cloaca Width (3.67 vs 3.58), Prefrontal Width (1.95 vs 2.04), Largest Supraoccular Width (1.25 vs 1.06), Finger III Length (1 vs 1.46), Ear to Eye Distance (3.9 vs 3.76), Head Width (5.43 vs 5.93), and Frontal Length (2.45 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia gracilis by SVL (63.66 vs 51.14), Mental to Vent Scale Count (123 vs 103), Midbody ScaleCount (34 vs 36), Strigae on Ten Scales (111 vs 100), Total Toe Length (6.68 vs 7.07), Scale Under Eye to Lip Distance (0.2 vs 0.13), Eye Length (1.57 vs 1.52), Arm Length (5.82 vs 5.54), Ear Width (0.39 vs 0.34), Rostral Width (1.53 vs 1.33), Rostral Height (0.84 vs 0.7), Head Length (7.8 vs 8.03), Mental Width (0.77 vs 0.9), Post Mental Width (1.54 vs 1.41), Cloaca Width (3.58 vs 3.67), Prefrontal Width (2.04 vs 1.95), Largest Supraoccular Width (1.06 vs 1.25), Finger III Length (1.46 vs 1), Ear to Eye Distance (3.76 vs 3.9), Head Width (5.93 vs 5.43), and Frontal Length (2.37 vs 2.45).
#>
#> From Sauresia habichi, we distinguish Sauresia manicula by Midbody ScaleCount (38-41 vs 37), Total Finger Lamella (18-19 vs 17), Strigae on Ten Scales (89-113 vs 119-150), Arm Length (6.61-7.04 vs 7.09-7.93), and Frontal Width (1.88-2.14 vs 2.55).
#>
#> From Sauresia manicula, we distinguish Sauresia habichi by Midbody ScaleCount (37 vs 38-41), Total Finger Lamella (17 vs 18-19), Strigae on Ten Scales (119-150 vs 89-113), Arm Length (7.09-7.93 vs 6.61-7.04), and Frontal Width (2.55 vs 1.88-2.14).
#>
#> From Sauresia habichi, we distinguish Sauresia pangnolae by Pattern (3-5 vs 1-2), Head Markings (1 vs 0), Dots in Lateral Band (0 vs 1), Mental to Vent Scale Count (122-125 vs 104-115), Eye Length (1.21-1.38 vs 1.51-1.93), and Ear Width (0.34-0.38 vs 0.44-0.61).
#>
#> From Sauresia pangnolae, we distinguish Sauresia habichi by Pattern (1-2 vs 3-5), Head Markings (0 vs 1), Dots in Lateral Band (1 vs 0), Mental to Vent Scale Count (104-115 vs 122-125), Eye Length (1.51-1.93 vs 1.21-1.38), and Ear Width (0.44-0.61 vs 0.34-0.38).
#>
#> From Sauresia habichi, we distinguish Sauresia sepsoides by Pattern (3-5 vs 1-2), Mental to Vent Scale Count (122-125 vs 108-119), Midbody ScaleCount (38-41 vs 35-37), and Total Finger Lamella (18-19 vs 14-17).
#>
#> From Sauresia sepsoides, we distinguish Sauresia habichi by Pattern (1-2 vs 3-5), Mental to Vent Scale Count (108-119 vs 122-125), Midbody ScaleCount (35-37 vs 38-41), and Total Finger Lamella (14-17 vs 18-19).
#>
#> From Sauresia habichi, we distinguish Sauresia synoria by SVL (50.5-59.7 vs 63.66), Pattern (3-5 vs 0), Midbody ScaleCount (38-41 vs 34), Scale Under Eye to Lip Distance (0.03-0.12 vs 0.2), Eye Length (1.21-1.38 vs 1.57), Arm Length (6.61-7.04 vs 5.82), Ear Width (0.34-0.38 vs 0.39), Rostral Width (1.43-1.46 vs 1.53), Rostral Height (0.59-0.8 vs 0.84), Mental Width (0.92-0.93 vs 0.77), Post Mental Width (1.18-1.39 vs 1.54), Finger III Length (1.37-1.4 vs 1.46), and Frontal Length (2.54-2.98 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia habichi by SVL (63.66 vs 50.5-59.7), Pattern (0 vs 3-5), Midbody ScaleCount (34 vs 38-41), Scale Under Eye to Lip Distance (0.2 vs 0.03-0.12), Eye Length (1.57 vs 1.21-1.38), Arm Length (5.82 vs 6.61-7.04), Ear Width (0.39 vs 0.34-0.38), Rostral Width (1.53 vs 1.43-1.46), Rostral Height (0.84 vs 0.59-0.8), Mental Width (0.77 vs 0.92-0.93), Post Mental Width (1.54 vs 1.18-1.39), Finger III Length (1.46 vs 1.37-1.4), and Frontal Length (2.37 vs 2.54-2.98).
#>
#> From Sauresia manicula, we distinguish Sauresia pangnolae by Pattern (3 vs 1-2), Dots in Lateral Band (0 vs 1), Mental to Vent Scale Count (123-129 vs 104-115), Midbody ScaleCount (37 vs 38-42), and Strigae on Ten Scales (119-150 vs 92-109).
#>
#> From Sauresia pangnolae, we distinguish Sauresia manicula by Pattern (1-2 vs 3), Dots in Lateral Band (1 vs 0), Mental to Vent Scale Count (104-115 vs 123-129), Midbody ScaleCount (38-42 vs 37), and Strigae on Ten Scales (92-109 vs 119-150).
#>
#> From Sauresia manicula, we distinguish Sauresia sepsoides by Pattern (3 vs 1-2), Mental to Vent Scale Count (123-129 vs 108-119), Strigae on Ten Scales (119-150 vs 94-114), Arm Length (7.09-7.93 vs 5.81-7.01), and Frontal Width (2.55 vs 2.04-2.35).
#>
#> From Sauresia sepsoides, we distinguish Sauresia manicula by Pattern (1-2 vs 3), Mental to Vent Scale Count (108-119 vs 123-129), Strigae on Ten Scales (94-114 vs 119-150), Arm Length (5.81-7.01 vs 7.09-7.93), and Frontal Width (2.04-2.35 vs 2.55).
#>
#> From Sauresia manicula, we distinguish Sauresia synoria by Pattern (3 vs 0), Midbody ScaleCount (37 vs 34), Total Finger Lamella (17 vs 18), Strigae on Ten Scales (119-150 vs 111), Scale Under Eye to Lip Distance (0.1-0.13 vs 0.2), Arm Length (7.09-7.93 vs 5.82), Mental Width (0.88-1.15 vs 0.77), Post Mental Width (1.27-1.49 vs 1.54), Largest Supraoccular Width (1.11-1.39 vs 1.06), Ear to Eye Distance (4.03-5.17 vs 3.76), and Frontal Length (2.59-3.13 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia manicula by Pattern (0 vs 3), Midbody ScaleCount (34 vs 37), Total Finger Lamella (18 vs 17), Strigae on Ten Scales (111 vs 119-150), Scale Under Eye to Lip Distance (0.2 vs 0.1-0.13), Arm Length (5.82 vs 7.09-7.93), Mental Width (0.77 vs 0.88-1.15), Post Mental Width (1.54 vs 1.27-1.49), Largest Supraoccular Width (1.06 vs 1.11-1.39), Ear to Eye Distance (3.76 vs 4.03-5.17), and Frontal Length (2.37 vs 2.59-3.13).
#>
#> From Sauresia pangnolae, we distinguish Sauresia sepsoides by Dots in Lateral Band (1 vs 0), and Midbody ScaleCount (38-42 vs 35-37).
#>
#> From Sauresia sepsoides, we distinguish Sauresia pangnolae by Dots in Lateral Band (0 vs 1), and Midbody ScaleCount (35-37 vs 38-42).
#>
#> From Sauresia pangnolae, we distinguish Sauresia synoria by Pattern (1-2 vs 0), Head Markings (0 vs 1), Dots in Lateral Band (1 vs 0), Mental to Vent Scale Count (104-115 vs 123), Midbody ScaleCount (38-42 vs 34), Strigae on Ten Scales (92-109 vs 111), Total Toe Length (7.42-8.82 vs 6.68), Scale Under Eye to Lip Distance (0.07-0.12 vs 0.2), Arm Length (6.78-7.95 vs 5.82), Ear Width (0.44-0.61 vs 0.39), Head Length (8.3-10.1 vs 7.8), Mental Width (0.79-1.27 vs 0.77), Cloaca Width (3.66-4.2 vs 3.58), Largest Supraoccular Width (1.15-1.49 vs 1.06), Ear to Eye Distance (4.04-4.97 vs 3.76), Head Width (6.24-7.15 vs 5.93), and Frontal Length (2.6-3.6 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia pangnolae by Pattern (0 vs 1-2), Head Markings (1 vs 0), Dots in Lateral Band (0 vs 1), Mental to Vent Scale Count (123 vs 104-115), Midbody ScaleCount (34 vs 38-42), Strigae on Ten Scales (111 vs 92-109), Total Toe Length (6.68 vs 7.42-8.82), Scale Under Eye to Lip Distance (0.2 vs 0.07-0.12), Arm Length (5.82 vs 6.78-7.95), Ear Width (0.39 vs 0.44-0.61), Head Length (7.8 vs 8.3-10.1), Mental Width (0.77 vs 0.79-1.27), Cloaca Width (3.58 vs 3.66-4.2), Largest Supraoccular Width (1.06 vs 1.15-1.49), Ear to Eye Distance (3.76 vs 4.04-4.97), Head Width (5.93 vs 6.24-7.15), and Frontal Length (2.37 vs 2.6-3.6).
#>
#> From Sauresia sepsoides, we distinguish Sauresia synoria by Pattern (1-2 vs 0), Mental to Vent Scale Count (108-119 vs 123), Midbody ScaleCount (35-37 vs 34), Total Finger Lamella (14-17 vs 18), Scale Under Eye to Lip Distance (0.11-0.19 vs 0.2), Mental Width (0.78-1.11 vs 0.77), Post Mental Width (1.12-1.43 vs 1.54), Finger III Length (1.03-1.38 vs 1.46), and Frontal Length (2.57-3.27 vs 2.37).
#>
#> From Sauresia synoria, we distinguish Sauresia sepsoides by Pattern (0 vs 1-2), Mental to Vent Scale Count (123 vs 108-119), Midbody ScaleCount (34 vs 35-37), Total Finger Lamella (18 vs 14-17), Scale Under Eye to Lip Distance (0.2 vs 0.11-0.19), Mental Width (0.77 vs 0.78-1.11), Post Mental Width (1.54 vs 1.12-1.43), Finger III Length (1.46 vs 1.03-1.38), and Frontal Length (2.37 vs 2.57-3.27).
#>
#>
#> The following groups could not be separated by any trait:
#> Sauresia agramma vs Wetmorena surda
#> Sauresia cayemitae vs Wetmorena surda
#> Sauresia gracilis vs Wetmorena surda
#> Sauresia habichi vs Wetmorena surda
#> Sauresia manicula vs Wetmorena surda
#> Sauresia pangnolae vs Wetmorena surda
#> Sauresia sepsoides vs Wetmorena surda
#> Sauresia synoria vs Wetmorena surdadocument_trait_range_table(): Create a table showing
trait ranges for all groups
Including the averages and number of samples for each trait is optional
document_trait_range_table(
sauresia_morpho3,
grouped_by = "Species",
trait_columns = c("SVL", "Pattern", "Head Markings", "Nuchal Lines", "Dots in Lateral Band",
"Mental to Vent Scale Count", "Midbody ScaleCount", "Total Finger Lamella",
"Strigae on Ten Scales", "Total Toe Length", "Scale Under Eye to Lip Distance",
"Eye Length", "Arm Length", "Ear Width", "Rostral Width", "Rostral Height",
"Head Length", "Mental Width", "Post Mental Width", "Cloaca Width",
"Prefrontal Width", "Largest Supraoccular Width", "Finger III Length",
"Ear to Eye Distance", "Head Width", "Frontal Width", "Frontal Length"),
include_counts = TRUE,
include_averages = TRUE)
#> # A tibble: 9 × 29
#> Species count SVL_range Pattern_range `Head Markings_range`
#> <chr> <int> <chr> <chr> <chr>
#> 1 Sauresia agramma 4 49.4-69.1 (59.27… 0-1 (0.5) (n… 0-1 (0.25) (n=4)
#> 2 Sauresia cayemitae 6 47.8-58.1 (53.18… 2-5 (4) (n=6) 1 (1) (n=6)
#> 3 Sauresia gracilis 1 51.14 (51.14) (n… N/A 1 (1) (n=1)
#> 4 Sauresia habichi 2 50.5-59.7 (55.1)… 3-5 (4) (n=2) 1 (1) (n=2)
#> 5 Sauresia manicula 2 59.6-69 (64.3) (… 3 (3) (n=2) N/A
#> 6 Sauresia pangnolae 4 54.3-66.7 (60.35… 1-2 (1.25) (… 0 (0) (n=4)
#> 7 Sauresia sepsoides 27 32.75-65.2 (56.2… 1-2 (1.64) (… 0-1 (0.36) (n=11)
#> 8 Sauresia synoria 1 63.66 (63.66) (n… 0 (0) (n=1) 1 (1) (n=1)
#> 9 Wetmorena surda 1 N/A N/A N/A
#> # ℹ 24 more variables: `Nuchal Lines_range` <chr>,
#> # `Dots in Lateral Band_range` <chr>,
#> # `Mental to Vent Scale Count_range` <chr>, `Midbody ScaleCount_range` <chr>,
#> # `Total Finger Lamella_range` <chr>, `Strigae on Ten Scales_range` <chr>,
#> # `Total Toe Length_range` <chr>,
#> # `Scale Under Eye to Lip Distance_range` <chr>, `Eye Length_range` <chr>,
#> # `Arm Length_range` <chr>, `Ear Width_range` <chr>, …document_appendix_section(): Create an
Appendix section for each group
document_appendix_section(
sauresia_morpho3,
grouped_by = "Species",
country_code_col = "Country",
region_col = "Province",
locality_col = "Locality",
lat_col = "Latitude",
long_col = "Longitude",
elevation_col = "Elevation",
institution_col = "Museum",
number_col = "Number")
#> Sauresia agramma (n=4): ANSP 38686, 38687, 38688 (, , ; N/A, N/A, N/Am). ANSP 38685 (Haiti, Sud-Est, Morne D'Enfer; 18.330052, -72.37095, 1433m).
#>
#> Sauresia cayemitae (n=6): ANSP 38691 (Haiti, Dept. de la Grand'Anse, Pestel 5.0 km S of; 18.513286, -73.784632, 300m). ANSP 38673 (Haiti, Grand'Anse, Grande Cayemite (helipad-camp); 18.63316, -73.755241, 74m). ANSP 38674, 38675, 38676 (Haiti, Grand'Anse, Grande Cayemite (waypoint 166); 18.635615, -73.751749, 38m). SBH 274212 (Haiti, Grand'Anse, Grande Cayemite (waypoint 166); 18.635615, -73.751749, 38m).
#>
#> Sauresia gracilis (n=1): UNSM 328852 (Haiti, Dept. du Sud, Port Salut 10.3 km NW; 18.140859, -73.967801, 10m).
#>
#> Sauresia habichi (n=2): ANSP 38681, 38683 (Haiti, Dept. de la Grand'Anse, Marche Leon 8.0 km S of; 18.516777, -74.083109, 435m).
#>
#> Sauresia manicula (n=2): ANSP 38667, 38668 (Haiti, L'Ouest, Berry; 18.307945, -72.253894, 1630m).
#>
#> Sauresia pangnolae (n=4): ANSP 38663, 38664 (Haiti, Dept. de la Grand'Anse, Baraderes 8.0 km SSW of; 18.44032, -73.667556, 420m). ANSP 38690 (Haiti, Dept. de la Grand'Anse, Pestel 11.8 km S of; 18.479421, -73.78744, 550m). ANSP 38684 (Haiti, Nippes, Morne Bois Pangnol; 18.418689, -73.775122, 1170m).
#>
#> Sauresia sepsoides (n=27): ANSP 38666 (Dominican Republic, Duarte Prov., Batez Piedra on west side of Rio Pazabo; 19.06997, -69.90815, 35m). SBH 193149 (Dominican Republic, Duarte Prov., Southern slopes of Loma Quita Espuela; N/A, N/A, 775m). SBH 267773 (Dominican Republic, Hato Mayor, 14.1 km W El Valle; Lat: 19d0.393' N Long: 69d29.333' W; N/A, N/A, 193m). UNSM 328850, 328851 (Dominican Republic, Hato Mayor, El Valle ca 15 km W (on road to Trepada Alta); N/A, N/A, N/Am). UNSM 328846 (Dominican Republic, Hato Mayor, Sabana De La Mar 9.5 km W (airline) in Los Haitises; 19.05293, -69.47899, N/Am). ANSP 38678 (Dominican Republic, La Altagracia, La Zanga 7.5 km W of (at Rio Maimon); N/A, N/A, 25m). ANSP 38706, 38707, 38708, 38709 (Dominican Republic, Los Tabucos, Tenares 8.8 km N thence 0.5 km W (Salcedo Prov.); N/A, N/A, 455m). SBH 266754 (Dominican Republic, Monte Plata, 6km S Los Limones; N/A, N/A, 305m). SBH 266748, 266749, 266750 (Dominican Republic, Monte Plata, Los Limones 3km S; N/A, N/A, 275m). SBH 266746 (Dominican Republic, Monte Plata, Los Limones footpath N of town; N/A, N/A, 197m). SBH 267754, 267755, 267756, 267757, 267758 (Dominican Republic, Monte Plata, ca. 1 km SW Los Limones; Lat: 19d1.119' N Long: 69d44.165' W; 19.01932, -69.73766, 250m). ANSP 38680 (Dominican Republic, Monte Plata Prov., Majagual 4.3 km N of; 19.07539, -69.82842, 90m). SBH 267780, 267781 (Dominican Republic, Parque Nacional Los Haitises, 1.2 km S Naranjo Arriba; Lat: 19d4.0' N Long: 69d34.276' W; 19.06667, -69.57127, 150m). ANSP 38670, 38671, 38672 (Dominican Republic, Sanchez Ramirez Prov., Cotui 8.6 km NE of thence 8.1 km east (=El Aguacate); 19.1037, -70.0531, 35m).
#>
#> Sauresia synoria (n=1): SBH 160343 (Dominican Republic, Pedernales, Pedernales 22 km N at Rio Mulito; 18.1544, -71.7581, 274m).
#>
#> Wetmorena surda (n=1): SBH 266705 (Dominican Republic, Pedernales, N Los Arroyos; 18.2579, -71.7446, 1660m).